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Molecular & Cellular Proteomics

Advanced Search

  • Home
  • Articles
    • Current Issue
    • Papers in Press
    • Reviews and Minireviews
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  • Guidelines
    • Proteomic Identification
      • Checklist (PDF)
      • Instructions for Annotated Spectra
      • Tutorial (PDF)
    • Clinical Proteomics
      • Checklist (PDF)
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      • Checklist (PDF)
    • Targeted Proteomics
      • Checklist (PDF)
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      • Checklist (PDF)
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Index by author

October 2019; Volume 18,Issue 10
  • A
  • B
  • C
  • D
  • E
  • F
  • G
  • H
  • I
  • J
  • K
  • L
  • M
  • N
  • O
  • P
  • Q
  • R
  • S
  • T
  • U
  • V
  • W
  • X
  • Y
  • Z

A

  1. Al-Mismar, Rasha

    1. A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      You have access
      A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      Anja M. Billing, Shaima S. Dib, Aditya M. Bhagwat, Israel T. da Silva, Rodrigo D. Drummond, Shahina Hayat, Rasha Al-Mismar, Hisham Ben-Hamidane, Neha Goswami, Kasper Engholm-Keller, Martin R. Larsen, Karsten Suhre, Arash Rafii and Johannes Graumann
      Molecular & Cellular Proteomics October 1, 2019, First published on July 22, 2019, 18 (10) 1950-1966; https://doi.org/10.1074/mcp.RA119.001356

      In this integrative, multi-omics study we characterized the differentiation of human embryonic stem cells into mesenchymal stem cells using transcriptomics, quantitative MS-based proteomics and phosphoproteomics. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation with AHNAK hypothesized to be a defining factor in MSC biology. Additional central findings include two distinct expression waves of developmental HOX genes as well as an AGO2-to-AGO3 switch in gene silencing.

B

  1. Bajrami, Besnik

    1. Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS
      You have access
      Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS
      Malvina Papanastasiou, James Mullahoo, Katherine C. DeRuff, Besnik Bajrami, Ioannis Karageorgos, Stephen E. Johnston, Ryan Peckner, Samuel A. Myers, Steven A. Carr and Jacob D. Jaffe
      Molecular & Cellular Proteomics October 1, 2019, First published on August 13, 2019, 18 (10) 2089-2098; https://doi.org/10.1074/mcp.RA119.001325

      Cathepsin-L, a protease known to proteolyse histone tails in cells, is introduced as a novel enzyme for HX-MS. Cathepsin-L generates overlapping N-terminal peptides, improving coverage of histone tails that are poorly represented in HX-MS employing pepsin alone. Cathepsin-L/pepsin is employed to investigate in-solution dynamics of H3 and H4 monomers. Rapid deuteration of the tails is indicative of unfolded polypeptides, whereas extensive bimodal distributions detected in the histone-folds reveal cooperative unfolding events.

  2. Bartkowiak-Kaczmarek, Anna

    1. Stress-induced Changes in the S-palmitoylation and S-nitrosylation of Synaptic Proteins
      You have access
      Stress-induced Changes in the S-palmitoylation and S-nitrosylation of Synaptic Proteins
      Monika Zareba-Koziol, Anna Bartkowiak-Kaczmarek, Izabela Figiel, Adam Krzystyniak, Tomasz Wojtowicz, Monika Bijata and Jakub Wlodarczyk
      Molecular & Cellular Proteomics October 1, 2019, First published on July 16, 2019, 18 (10) 1916-1938; https://doi.org/10.1074/mcp.RA119.001581

      To improve simultaneous S-palmitoylation and S-nitrosylation site profiling, we developed a novel mass spectrometry-based strategy Palmitoylation And Nitrosylation Interplay Monitoring (PANIMoni). Using this approach we evaluated dynamic, site-specific changes in two important cysteine modifications, S-PALM and S-NO, in a mouse model of chronic stress. High-throughput analysis provided valuable insight into chronic, stress-induced remodeling of the synaptic proteome. Based on the obtained data, we postulate that the mechanism underlying chronic stress involves mutual competition between S-PALM and S-NO for modification sites.

  3. Batruch, Ihor

    1. Defining Protein Pattern Differences Among Molecular Subtypes of Diffuse Gliomas Using Mass Spectrometry
      You have access
      Defining Protein Pattern Differences Among Molecular Subtypes of Diffuse Gliomas Using Mass Spectrometry
      Ugljesa Djuric, K. H. Brian Lam, Jennifer Kao, Ihor Batruch, Stefan Jevtic, Michail-Dimitrios Papaioannou and Phedias Diamandis
      Molecular & Cellular Proteomics October 1, 2019, First published on July 28, 2019, 18 (10) 2029-2043; https://doi.org/10.1074/mcp.RA119.001521

      Gliomas represent the most common brain tumor type. Molecular and global omics are becoming powerful tools for tumor subclassification that will facilitate more subtype-specific treatment options for patients. Here, we demonstrate that proteomic-based subclassification of closely related gliomas, differentiated by IDH mutation and 1p19q chromosome codeletion status, is facilitated by tumor microdissections prior to mass spectrometry analysis. Identified protein modules are confirmed in tissue culture grown glioma stem cells and point to chloride transport and stress proteins as strong drivers of glioma molecular diversions.

  4. Ben-Hamidane, Hisham

    1. A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      You have access
      A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      Anja M. Billing, Shaima S. Dib, Aditya M. Bhagwat, Israel T. da Silva, Rodrigo D. Drummond, Shahina Hayat, Rasha Al-Mismar, Hisham Ben-Hamidane, Neha Goswami, Kasper Engholm-Keller, Martin R. Larsen, Karsten Suhre, Arash Rafii and Johannes Graumann
      Molecular & Cellular Proteomics October 1, 2019, First published on July 22, 2019, 18 (10) 1950-1966; https://doi.org/10.1074/mcp.RA119.001356

      In this integrative, multi-omics study we characterized the differentiation of human embryonic stem cells into mesenchymal stem cells using transcriptomics, quantitative MS-based proteomics and phosphoproteomics. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation with AHNAK hypothesized to be a defining factor in MSC biology. Additional central findings include two distinct expression waves of developmental HOX genes as well as an AGO2-to-AGO3 switch in gene silencing.

  5. Bensaddek, Dalila

    1. Multibatch TMT Reveals False Positives, Batch Effects and Missing Values
      Open Access
      Multibatch TMT Reveals False Positives, Batch Effects and Missing Values
      Alejandro Brenes, Jens Hukelmann, Dalila Bensaddek and Angus I. Lamond
      Molecular & Cellular Proteomics October 1, 2019, First published on July 22, 2019, 18 (10) 1967-1980; https://doi.org/10.1074/mcp.RA119.001472

      Analysis of 24 TMT 10-plex batches revealed an inflation in missing values and reduced inter-batch accuracy as multiple TMT batches are integrated. Our data also highlights the incidence of false positives exemplified by Y chromosome peptides being detected in female channels. The Y chromosome peptides were then used to quantify the effects of coisolation and reporter ion interference on TMT quantification and to propose an experimental design that would minimise cross population reporter ion interference.

  6. Bhagwat, Aditya M.

    1. A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      You have access
      A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      Anja M. Billing, Shaima S. Dib, Aditya M. Bhagwat, Israel T. da Silva, Rodrigo D. Drummond, Shahina Hayat, Rasha Al-Mismar, Hisham Ben-Hamidane, Neha Goswami, Kasper Engholm-Keller, Martin R. Larsen, Karsten Suhre, Arash Rafii and Johannes Graumann
      Molecular & Cellular Proteomics October 1, 2019, First published on July 22, 2019, 18 (10) 1950-1966; https://doi.org/10.1074/mcp.RA119.001356

      In this integrative, multi-omics study we characterized the differentiation of human embryonic stem cells into mesenchymal stem cells using transcriptomics, quantitative MS-based proteomics and phosphoproteomics. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation with AHNAK hypothesized to be a defining factor in MSC biology. Additional central findings include two distinct expression waves of developmental HOX genes as well as an AGO2-to-AGO3 switch in gene silencing.

  7. Bijata, Monika

    1. Stress-induced Changes in the S-palmitoylation and S-nitrosylation of Synaptic Proteins
      You have access
      Stress-induced Changes in the S-palmitoylation and S-nitrosylation of Synaptic Proteins
      Monika Zareba-Koziol, Anna Bartkowiak-Kaczmarek, Izabela Figiel, Adam Krzystyniak, Tomasz Wojtowicz, Monika Bijata and Jakub Wlodarczyk
      Molecular & Cellular Proteomics October 1, 2019, First published on July 16, 2019, 18 (10) 1916-1938; https://doi.org/10.1074/mcp.RA119.001581

      To improve simultaneous S-palmitoylation and S-nitrosylation site profiling, we developed a novel mass spectrometry-based strategy Palmitoylation And Nitrosylation Interplay Monitoring (PANIMoni). Using this approach we evaluated dynamic, site-specific changes in two important cysteine modifications, S-PALM and S-NO, in a mouse model of chronic stress. High-throughput analysis provided valuable insight into chronic, stress-induced remodeling of the synaptic proteome. Based on the obtained data, we postulate that the mechanism underlying chronic stress involves mutual competition between S-PALM and S-NO for modification sites.

  8. Billing, Anja M.

    1. A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      You have access
      A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      Anja M. Billing, Shaima S. Dib, Aditya M. Bhagwat, Israel T. da Silva, Rodrigo D. Drummond, Shahina Hayat, Rasha Al-Mismar, Hisham Ben-Hamidane, Neha Goswami, Kasper Engholm-Keller, Martin R. Larsen, Karsten Suhre, Arash Rafii and Johannes Graumann
      Molecular & Cellular Proteomics October 1, 2019, First published on July 22, 2019, 18 (10) 1950-1966; https://doi.org/10.1074/mcp.RA119.001356

      In this integrative, multi-omics study we characterized the differentiation of human embryonic stem cells into mesenchymal stem cells using transcriptomics, quantitative MS-based proteomics and phosphoproteomics. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation with AHNAK hypothesized to be a defining factor in MSC biology. Additional central findings include two distinct expression waves of developmental HOX genes as well as an AGO2-to-AGO3 switch in gene silencing.

  9. Blanco, Francisco J.

    1. Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      You have access
      Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      Patricia Fernández-Puente, Lucía González-Rodríguez, Valentina Calamia, Florencia Picchi, Lucía Lourido, María Camacho-Encina, Natividad Oreiro, Beatriz Rocha, Rocío Paz-González, Anabel Marina, Carlos García, Francisco J. Blanco and Cristina Ruiz-Romero
      Molecular & Cellular Proteomics October 1, 2019, First published on July 27, 2019, 18 (10) 2018-2028; https://doi.org/10.1074/mcp.RA119.001554

      Osteoarthritis (OA) is a disease primarily characterized by the loss of cartilage extracellular matrix. We have followed a peptidomic strategy to identify endogenous peptides (neopeptides) released from healthy and OA human knee and hip articular cartilage, which may serve as disease markers. This study provides a comprehensive neopeptidomic profile of healthy and diseased tissues, and the identification and validation of a panel of eight endogenous peptides that are differentially released from the extracellular matrix because of the pathogenic process.

  10. Borges, Chad R.

    1. Delta-S-Cys-Albumin: A Lab Test that Quantifies Cumulative Exposure of Archived Human Blood Plasma and Serum Samples to Thawed Conditions
      Open Access
      Delta-S-Cys-Albumin: A Lab Test that Quantifies Cumulative Exposure of Archived Human Blood Plasma and Serum Samples to Thawed Conditions
      Joshua W. Jeffs, Nilojan Jehanathan, Stephanie M. F. Thibert, Shadi Ferdosi, Linda Pham, Zachary T. Wilson, Christian Breburda and Chad R. Borges
      Molecular & Cellular Proteomics October 1, 2019, First published on July 19, 2019, 18 (10) 2121-2137; https://doi.org/10.1074/mcp.TIR119.001659

      ΔS-Cys-Albumin, an endogenous marker of plasma and serum (P/S) exposure to thawed conditions (> −30 °C) based on the ex vivo S-cysteinylation (oxidizability) of albumin was developed. Average values in fresh P/S samples from a population of nonacute cardiac patients were determined. The multireaction mechanism that drives changes in albumin S-cysteinylation is known and the rate law for it has been established and accurately modeled in P/S. Measurement of ΔS-Cys-Albumin in unknown samples facilitates estimation of thawed-state exposure times.

  11. Breburda, Christian

    1. Delta-S-Cys-Albumin: A Lab Test that Quantifies Cumulative Exposure of Archived Human Blood Plasma and Serum Samples to Thawed Conditions
      Open Access
      Delta-S-Cys-Albumin: A Lab Test that Quantifies Cumulative Exposure of Archived Human Blood Plasma and Serum Samples to Thawed Conditions
      Joshua W. Jeffs, Nilojan Jehanathan, Stephanie M. F. Thibert, Shadi Ferdosi, Linda Pham, Zachary T. Wilson, Christian Breburda and Chad R. Borges
      Molecular & Cellular Proteomics October 1, 2019, First published on July 19, 2019, 18 (10) 2121-2137; https://doi.org/10.1074/mcp.TIR119.001659

      ΔS-Cys-Albumin, an endogenous marker of plasma and serum (P/S) exposure to thawed conditions (> −30 °C) based on the ex vivo S-cysteinylation (oxidizability) of albumin was developed. Average values in fresh P/S samples from a population of nonacute cardiac patients were determined. The multireaction mechanism that drives changes in albumin S-cysteinylation is known and the rate law for it has been established and accurately modeled in P/S. Measurement of ΔS-Cys-Albumin in unknown samples facilitates estimation of thawed-state exposure times.

  12. Brenes, Alejandro

    1. Multibatch TMT Reveals False Positives, Batch Effects and Missing Values
      Open Access
      Multibatch TMT Reveals False Positives, Batch Effects and Missing Values
      Alejandro Brenes, Jens Hukelmann, Dalila Bensaddek and Angus I. Lamond
      Molecular & Cellular Proteomics October 1, 2019, First published on July 22, 2019, 18 (10) 1967-1980; https://doi.org/10.1074/mcp.RA119.001472

      Analysis of 24 TMT 10-plex batches revealed an inflation in missing values and reduced inter-batch accuracy as multiple TMT batches are integrated. Our data also highlights the incidence of false positives exemplified by Y chromosome peptides being detected in female channels. The Y chromosome peptides were then used to quantify the effects of coisolation and reporter ion interference on TMT quantification and to propose an experimental design that would minimise cross population reporter ion interference.

C

  1. Calamia, Valentina

    1. Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      You have access
      Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      Patricia Fernández-Puente, Lucía González-Rodríguez, Valentina Calamia, Florencia Picchi, Lucía Lourido, María Camacho-Encina, Natividad Oreiro, Beatriz Rocha, Rocío Paz-González, Anabel Marina, Carlos García, Francisco J. Blanco and Cristina Ruiz-Romero
      Molecular & Cellular Proteomics October 1, 2019, First published on July 27, 2019, 18 (10) 2018-2028; https://doi.org/10.1074/mcp.RA119.001554

      Osteoarthritis (OA) is a disease primarily characterized by the loss of cartilage extracellular matrix. We have followed a peptidomic strategy to identify endogenous peptides (neopeptides) released from healthy and OA human knee and hip articular cartilage, which may serve as disease markers. This study provides a comprehensive neopeptidomic profile of healthy and diseased tissues, and the identification and validation of a panel of eight endogenous peptides that are differentially released from the extracellular matrix because of the pathogenic process.

  2. Camacho-Encina, María

    1. Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      You have access
      Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      Patricia Fernández-Puente, Lucía González-Rodríguez, Valentina Calamia, Florencia Picchi, Lucía Lourido, María Camacho-Encina, Natividad Oreiro, Beatriz Rocha, Rocío Paz-González, Anabel Marina, Carlos García, Francisco J. Blanco and Cristina Ruiz-Romero
      Molecular & Cellular Proteomics October 1, 2019, First published on July 27, 2019, 18 (10) 2018-2028; https://doi.org/10.1074/mcp.RA119.001554

      Osteoarthritis (OA) is a disease primarily characterized by the loss of cartilage extracellular matrix. We have followed a peptidomic strategy to identify endogenous peptides (neopeptides) released from healthy and OA human knee and hip articular cartilage, which may serve as disease markers. This study provides a comprehensive neopeptidomic profile of healthy and diseased tissues, and the identification and validation of a panel of eight endogenous peptides that are differentially released from the extracellular matrix because of the pathogenic process.

  3. Cao, Ye

    1. Multidimensional Proteomics Identifies Declines in Protein Homeostasis and Mitochondria as Early Signals for Normal Aging and Age-associated Disease in <em>Drosophila</em>
      You have access
      Multidimensional Proteomics Identifies Declines in Protein Homeostasis and Mitochondria as Early Signals for Normal Aging and Age-associated Disease in Drosophila
      Lu Yang, Ye Cao, Jing Zhao, Yanshan Fang, Nan Liu and Yaoyang Zhang
      Molecular & Cellular Proteomics October 1, 2019, First published on August 21, 2019, 18 (10) 2078-2088; https://doi.org/10.1074/mcp.RA119.001621

      Yang et al. have profiled the snapshot and dynamics of the proteomes from Drosophila somatic and reproductive tissues during aging, revealing both tissue-specific and common pathways that are modulated with age. Analysis of proteome dynamics demonstrates that the global protein synthesis, particularly for those proteins functionally related to proteostasis and mitochondria, is down-regulated during normal aging, and that this decline becomes dramatically enhanced in the Drosophila model of human Parkinson's disease.

  4. Carr, Steven A.

    1. Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS
      You have access
      Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS
      Malvina Papanastasiou, James Mullahoo, Katherine C. DeRuff, Besnik Bajrami, Ioannis Karageorgos, Stephen E. Johnston, Ryan Peckner, Samuel A. Myers, Steven A. Carr and Jacob D. Jaffe
      Molecular & Cellular Proteomics October 1, 2019, First published on August 13, 2019, 18 (10) 2089-2098; https://doi.org/10.1074/mcp.RA119.001325

      Cathepsin-L, a protease known to proteolyse histone tails in cells, is introduced as a novel enzyme for HX-MS. Cathepsin-L generates overlapping N-terminal peptides, improving coverage of histone tails that are poorly represented in HX-MS employing pepsin alone. Cathepsin-L/pepsin is employed to investigate in-solution dynamics of H3 and H4 monomers. Rapid deuteration of the tails is indicative of unfolded polypeptides, whereas extensive bimodal distributions detected in the histone-folds reveal cooperative unfolding events.

  5. Chai, Wengang

    1. Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Open Access
      Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Nian Wu, Lisete M. Silva, Yan Liu, Yibing Zhang, Chao Gao, Fuming Zhang, Li Fu, Yanfei Peng, Robert Linhardt, Toshisuke Kawasaki, Barbara Mulloy, Wengang Chai and Ten Feizi
      Molecular & Cellular Proteomics October 1, 2019, First published on July 15, 2019, 18 (10) 1981-2002; https://doi.org/10.1074/mcp.RA119.001309

      R-10G antigen of human iPS and ES cells has been assigned as a unique mono-sulfated glycan. We highlight its relationship to a known bioactive glycan sequence, the ligand on high endothelial venules for the lymphocyte homing receptor, L-selectin. Details of the sequences of four other glycan antigens on the podocalyxin are re-evaluated and ambiguities resolved. Regulation of biosynthesis and possible involvements of these glycans in podocalyxin-signaling in stem cells are discussed.

  6. Chang, Kai-Ping

    1. Proteomic Profiling of Paired Interstitial Fluids Reveals Dysregulated Pathways and Salivary NID1 as a Biomarker of Oral Cavity Squamous Cell Carcinoma
      You have access
      Proteomic Profiling of Paired Interstitial Fluids Reveals Dysregulated Pathways and Salivary NID1 as a Biomarker of Oral Cavity Squamous Cell Carcinoma
      Chia-Wei Hsu, Kai-Ping Chang, Yenlin Huang, Hao-Ping Liu, Pei-Chun Hsueh, Po-Wen Gu, Wei-Chen Yen and Chih-Ching Wu
      Molecular & Cellular Proteomics October 1, 2019, First published on July 17, 2019, 18 (10) 1939-1949; https://doi.org/10.1074/mcp.RA119.001654

      Oral cavity squamous cell carcinoma (OSCC) is frequently diagnosed at an advanced stage, leading to poor prognosis and high mortality rate. To develop method for OSCC detection, proteome of tumor interstitial fluids (TIFs) has been profiled. The proteins differentially expressed in TIFs were highly associated with aminoacyl tRNA biosynthesis pathway. Importantly, nidogen-1 is a potential diagnostic and/or prognostic biomarker. The results suggest that TIF analysis facilitates understanding of OSCC microenvironment and discovery of biomarker candidates.

  7. Cheng, Zhongyi

    1. <em>Sc</em>CobB2-mediated Lysine Desuccinylation Regulates Protein Biosynthesis and Carbon Metabolism in <em>Streptomyces coelicolor</em>
      You have access
      ScCobB2-mediated Lysine Desuccinylation Regulates Protein Biosynthesis and Carbon Metabolism in Streptomyces coelicolor
      Hong Zhang, Peng Li, Shuangxi Ren, Zhongyi Cheng, Guoping Zhao and Wei Zhao
      Molecular & Cellular Proteomics October 1, 2019, First published on July 23, 2019, 18 (10) 2003-2017; https://doi.org/10.1074/mcp.RA118.001298

      Lysine succinylation is a prevalent protein modification that regulates multiple critical cellular processes. Here, we performed a quantitative succinylome analysis in the model soil bacterium Streptomyces coelicolor after characterization of a specific desuccinylase ScCobB2. Comparison of the ΔScCobB2 to the wild-type succinylome identified a total of 673 unique succinylated sites, and among which, 144 protein sites are statistically hypersuccinylated in ΔScCobB2 cells. Analyses of these hypersuccinylated proteins suggested they are enriched in two major pathways, protein biosynthesis and carbon metabolism. We propose that ScCobB2 has critical regulatory roles in S. coelicolor cellular physiology.

D

  1. da Silva, Israel T.

    1. A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      You have access
      A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      Anja M. Billing, Shaima S. Dib, Aditya M. Bhagwat, Israel T. da Silva, Rodrigo D. Drummond, Shahina Hayat, Rasha Al-Mismar, Hisham Ben-Hamidane, Neha Goswami, Kasper Engholm-Keller, Martin R. Larsen, Karsten Suhre, Arash Rafii and Johannes Graumann
      Molecular & Cellular Proteomics October 1, 2019, First published on July 22, 2019, 18 (10) 1950-1966; https://doi.org/10.1074/mcp.RA119.001356

      In this integrative, multi-omics study we characterized the differentiation of human embryonic stem cells into mesenchymal stem cells using transcriptomics, quantitative MS-based proteomics and phosphoproteomics. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation with AHNAK hypothesized to be a defining factor in MSC biology. Additional central findings include two distinct expression waves of developmental HOX genes as well as an AGO2-to-AGO3 switch in gene silencing.

  2. DeRuff, Katherine C.

    1. Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS
      You have access
      Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS
      Malvina Papanastasiou, James Mullahoo, Katherine C. DeRuff, Besnik Bajrami, Ioannis Karageorgos, Stephen E. Johnston, Ryan Peckner, Samuel A. Myers, Steven A. Carr and Jacob D. Jaffe
      Molecular & Cellular Proteomics October 1, 2019, First published on August 13, 2019, 18 (10) 2089-2098; https://doi.org/10.1074/mcp.RA119.001325

      Cathepsin-L, a protease known to proteolyse histone tails in cells, is introduced as a novel enzyme for HX-MS. Cathepsin-L generates overlapping N-terminal peptides, improving coverage of histone tails that are poorly represented in HX-MS employing pepsin alone. Cathepsin-L/pepsin is employed to investigate in-solution dynamics of H3 and H4 monomers. Rapid deuteration of the tails is indicative of unfolded polypeptides, whereas extensive bimodal distributions detected in the histone-folds reveal cooperative unfolding events.

  3. Diamandis, Phedias

    1. Defining Protein Pattern Differences Among Molecular Subtypes of Diffuse Gliomas Using Mass Spectrometry
      You have access
      Defining Protein Pattern Differences Among Molecular Subtypes of Diffuse Gliomas Using Mass Spectrometry
      Ugljesa Djuric, K. H. Brian Lam, Jennifer Kao, Ihor Batruch, Stefan Jevtic, Michail-Dimitrios Papaioannou and Phedias Diamandis
      Molecular & Cellular Proteomics October 1, 2019, First published on July 28, 2019, 18 (10) 2029-2043; https://doi.org/10.1074/mcp.RA119.001521

      Gliomas represent the most common brain tumor type. Molecular and global omics are becoming powerful tools for tumor subclassification that will facilitate more subtype-specific treatment options for patients. Here, we demonstrate that proteomic-based subclassification of closely related gliomas, differentiated by IDH mutation and 1p19q chromosome codeletion status, is facilitated by tumor microdissections prior to mass spectrometry analysis. Identified protein modules are confirmed in tissue culture grown glioma stem cells and point to chloride transport and stress proteins as strong drivers of glioma molecular diversions.

  4. Dib, Shaima S.

    1. A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      You have access
      A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      Anja M. Billing, Shaima S. Dib, Aditya M. Bhagwat, Israel T. da Silva, Rodrigo D. Drummond, Shahina Hayat, Rasha Al-Mismar, Hisham Ben-Hamidane, Neha Goswami, Kasper Engholm-Keller, Martin R. Larsen, Karsten Suhre, Arash Rafii and Johannes Graumann
      Molecular & Cellular Proteomics October 1, 2019, First published on July 22, 2019, 18 (10) 1950-1966; https://doi.org/10.1074/mcp.RA119.001356

      In this integrative, multi-omics study we characterized the differentiation of human embryonic stem cells into mesenchymal stem cells using transcriptomics, quantitative MS-based proteomics and phosphoproteomics. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation with AHNAK hypothesized to be a defining factor in MSC biology. Additional central findings include two distinct expression waves of developmental HOX genes as well as an AGO2-to-AGO3 switch in gene silencing.

  5. Djuric, Ugljesa

    1. Defining Protein Pattern Differences Among Molecular Subtypes of Diffuse Gliomas Using Mass Spectrometry
      You have access
      Defining Protein Pattern Differences Among Molecular Subtypes of Diffuse Gliomas Using Mass Spectrometry
      Ugljesa Djuric, K. H. Brian Lam, Jennifer Kao, Ihor Batruch, Stefan Jevtic, Michail-Dimitrios Papaioannou and Phedias Diamandis
      Molecular & Cellular Proteomics October 1, 2019, First published on July 28, 2019, 18 (10) 2029-2043; https://doi.org/10.1074/mcp.RA119.001521

      Gliomas represent the most common brain tumor type. Molecular and global omics are becoming powerful tools for tumor subclassification that will facilitate more subtype-specific treatment options for patients. Here, we demonstrate that proteomic-based subclassification of closely related gliomas, differentiated by IDH mutation and 1p19q chromosome codeletion status, is facilitated by tumor microdissections prior to mass spectrometry analysis. Identified protein modules are confirmed in tissue culture grown glioma stem cells and point to chloride transport and stress proteins as strong drivers of glioma molecular diversions.

  6. Drexler, Hannes C. A.

    1. Vascular Endothelial Receptor Tyrosine Phosphatase: Identification of Novel Substrates Related to Junctions and a Ternary Complex with EPHB4 and TIE2
      You have access
      Vascular Endothelial Receptor Tyrosine Phosphatase: Identification of Novel Substrates Related to Junctions and a Ternary Complex with EPHB4 and TIE2
      Hannes C. A. Drexler, Matthias Vockel, Christian Polaschegg, Maike Frye, Kevin Peters and Dietmar Vestweber
      Molecular & Cellular Proteomics October 1, 2019, First published on August 19, 2019, 18 (10) 2058-2077; https://doi.org/10.1074/mcp.RA119.001716

      The phosphoproteome of the endothelial receptor type tyrosine phosphatase VE-PTP has been identified for mouse endothelial cells by a substrate trapping approach and a second anti-phosphotyrosine affinity isolation approach. In agreement with the central role of VE-PTP as regulator of endothelial junctions, 29% of the identified substrate candidates were junction related. Besides the well characterized substrates Tie-2 and FGD5, the tyrosine kinase receptor EPHB4 was identified as novel substrate, which formed a ternary complex with VE-PTP and Tie-2.

  7. Drummond, Rodrigo D.

    1. A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      You have access
      A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      Anja M. Billing, Shaima S. Dib, Aditya M. Bhagwat, Israel T. da Silva, Rodrigo D. Drummond, Shahina Hayat, Rasha Al-Mismar, Hisham Ben-Hamidane, Neha Goswami, Kasper Engholm-Keller, Martin R. Larsen, Karsten Suhre, Arash Rafii and Johannes Graumann
      Molecular & Cellular Proteomics October 1, 2019, First published on July 22, 2019, 18 (10) 1950-1966; https://doi.org/10.1074/mcp.RA119.001356

      In this integrative, multi-omics study we characterized the differentiation of human embryonic stem cells into mesenchymal stem cells using transcriptomics, quantitative MS-based proteomics and phosphoproteomics. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation with AHNAK hypothesized to be a defining factor in MSC biology. Additional central findings include two distinct expression waves of developmental HOX genes as well as an AGO2-to-AGO3 switch in gene silencing.

E

  1. Engholm-Keller, Kasper

    1. A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      You have access
      A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      Anja M. Billing, Shaima S. Dib, Aditya M. Bhagwat, Israel T. da Silva, Rodrigo D. Drummond, Shahina Hayat, Rasha Al-Mismar, Hisham Ben-Hamidane, Neha Goswami, Kasper Engholm-Keller, Martin R. Larsen, Karsten Suhre, Arash Rafii and Johannes Graumann
      Molecular & Cellular Proteomics October 1, 2019, First published on July 22, 2019, 18 (10) 1950-1966; https://doi.org/10.1074/mcp.RA119.001356

      In this integrative, multi-omics study we characterized the differentiation of human embryonic stem cells into mesenchymal stem cells using transcriptomics, quantitative MS-based proteomics and phosphoproteomics. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation with AHNAK hypothesized to be a defining factor in MSC biology. Additional central findings include two distinct expression waves of developmental HOX genes as well as an AGO2-to-AGO3 switch in gene silencing.

F

  1. Fang, Yanshan

    1. Multidimensional Proteomics Identifies Declines in Protein Homeostasis and Mitochondria as Early Signals for Normal Aging and Age-associated Disease in <em>Drosophila</em>
      You have access
      Multidimensional Proteomics Identifies Declines in Protein Homeostasis and Mitochondria as Early Signals for Normal Aging and Age-associated Disease in Drosophila
      Lu Yang, Ye Cao, Jing Zhao, Yanshan Fang, Nan Liu and Yaoyang Zhang
      Molecular & Cellular Proteomics October 1, 2019, First published on August 21, 2019, 18 (10) 2078-2088; https://doi.org/10.1074/mcp.RA119.001621

      Yang et al. have profiled the snapshot and dynamics of the proteomes from Drosophila somatic and reproductive tissues during aging, revealing both tissue-specific and common pathways that are modulated with age. Analysis of proteome dynamics demonstrates that the global protein synthesis, particularly for those proteins functionally related to proteostasis and mitochondria, is down-regulated during normal aging, and that this decline becomes dramatically enhanced in the Drosophila model of human Parkinson's disease.

  2. Feizi, Ten

    1. Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Open Access
      Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Nian Wu, Lisete M. Silva, Yan Liu, Yibing Zhang, Chao Gao, Fuming Zhang, Li Fu, Yanfei Peng, Robert Linhardt, Toshisuke Kawasaki, Barbara Mulloy, Wengang Chai and Ten Feizi
      Molecular & Cellular Proteomics October 1, 2019, First published on July 15, 2019, 18 (10) 1981-2002; https://doi.org/10.1074/mcp.RA119.001309

      R-10G antigen of human iPS and ES cells has been assigned as a unique mono-sulfated glycan. We highlight its relationship to a known bioactive glycan sequence, the ligand on high endothelial venules for the lymphocyte homing receptor, L-selectin. Details of the sequences of four other glycan antigens on the podocalyxin are re-evaluated and ambiguities resolved. Regulation of biosynthesis and possible involvements of these glycans in podocalyxin-signaling in stem cells are discussed.

  3. Ferdosi, Shadi

    1. Delta-S-Cys-Albumin: A Lab Test that Quantifies Cumulative Exposure of Archived Human Blood Plasma and Serum Samples to Thawed Conditions
      Open Access
      Delta-S-Cys-Albumin: A Lab Test that Quantifies Cumulative Exposure of Archived Human Blood Plasma and Serum Samples to Thawed Conditions
      Joshua W. Jeffs, Nilojan Jehanathan, Stephanie M. F. Thibert, Shadi Ferdosi, Linda Pham, Zachary T. Wilson, Christian Breburda and Chad R. Borges
      Molecular & Cellular Proteomics October 1, 2019, First published on July 19, 2019, 18 (10) 2121-2137; https://doi.org/10.1074/mcp.TIR119.001659

      ΔS-Cys-Albumin, an endogenous marker of plasma and serum (P/S) exposure to thawed conditions (> −30 °C) based on the ex vivo S-cysteinylation (oxidizability) of albumin was developed. Average values in fresh P/S samples from a population of nonacute cardiac patients were determined. The multireaction mechanism that drives changes in albumin S-cysteinylation is known and the rate law for it has been established and accurately modeled in P/S. Measurement of ΔS-Cys-Albumin in unknown samples facilitates estimation of thawed-state exposure times.

  4. Fernández-Puente, Patricia

    1. Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      You have access
      Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      Patricia Fernández-Puente, Lucía González-Rodríguez, Valentina Calamia, Florencia Picchi, Lucía Lourido, María Camacho-Encina, Natividad Oreiro, Beatriz Rocha, Rocío Paz-González, Anabel Marina, Carlos García, Francisco J. Blanco and Cristina Ruiz-Romero
      Molecular & Cellular Proteomics October 1, 2019, First published on July 27, 2019, 18 (10) 2018-2028; https://doi.org/10.1074/mcp.RA119.001554

      Osteoarthritis (OA) is a disease primarily characterized by the loss of cartilage extracellular matrix. We have followed a peptidomic strategy to identify endogenous peptides (neopeptides) released from healthy and OA human knee and hip articular cartilage, which may serve as disease markers. This study provides a comprehensive neopeptidomic profile of healthy and diseased tissues, and the identification and validation of a panel of eight endogenous peptides that are differentially released from the extracellular matrix because of the pathogenic process.

  5. Figiel, Izabela

    1. Stress-induced Changes in the S-palmitoylation and S-nitrosylation of Synaptic Proteins
      You have access
      Stress-induced Changes in the S-palmitoylation and S-nitrosylation of Synaptic Proteins
      Monika Zareba-Koziol, Anna Bartkowiak-Kaczmarek, Izabela Figiel, Adam Krzystyniak, Tomasz Wojtowicz, Monika Bijata and Jakub Wlodarczyk
      Molecular & Cellular Proteomics October 1, 2019, First published on July 16, 2019, 18 (10) 1916-1938; https://doi.org/10.1074/mcp.RA119.001581

      To improve simultaneous S-palmitoylation and S-nitrosylation site profiling, we developed a novel mass spectrometry-based strategy Palmitoylation And Nitrosylation Interplay Monitoring (PANIMoni). Using this approach we evaluated dynamic, site-specific changes in two important cysteine modifications, S-PALM and S-NO, in a mouse model of chronic stress. High-throughput analysis provided valuable insight into chronic, stress-induced remodeling of the synaptic proteome. Based on the obtained data, we postulate that the mechanism underlying chronic stress involves mutual competition between S-PALM and S-NO for modification sites.

  6. Frye, Maike

    1. Vascular Endothelial Receptor Tyrosine Phosphatase: Identification of Novel Substrates Related to Junctions and a Ternary Complex with EPHB4 and TIE2
      You have access
      Vascular Endothelial Receptor Tyrosine Phosphatase: Identification of Novel Substrates Related to Junctions and a Ternary Complex with EPHB4 and TIE2
      Hannes C. A. Drexler, Matthias Vockel, Christian Polaschegg, Maike Frye, Kevin Peters and Dietmar Vestweber
      Molecular & Cellular Proteomics October 1, 2019, First published on August 19, 2019, 18 (10) 2058-2077; https://doi.org/10.1074/mcp.RA119.001716

      The phosphoproteome of the endothelial receptor type tyrosine phosphatase VE-PTP has been identified for mouse endothelial cells by a substrate trapping approach and a second anti-phosphotyrosine affinity isolation approach. In agreement with the central role of VE-PTP as regulator of endothelial junctions, 29% of the identified substrate candidates were junction related. Besides the well characterized substrates Tie-2 and FGD5, the tyrosine kinase receptor EPHB4 was identified as novel substrate, which formed a ternary complex with VE-PTP and Tie-2.

  7. Fu, Li

    1. Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Open Access
      Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Nian Wu, Lisete M. Silva, Yan Liu, Yibing Zhang, Chao Gao, Fuming Zhang, Li Fu, Yanfei Peng, Robert Linhardt, Toshisuke Kawasaki, Barbara Mulloy, Wengang Chai and Ten Feizi
      Molecular & Cellular Proteomics October 1, 2019, First published on July 15, 2019, 18 (10) 1981-2002; https://doi.org/10.1074/mcp.RA119.001309

      R-10G antigen of human iPS and ES cells has been assigned as a unique mono-sulfated glycan. We highlight its relationship to a known bioactive glycan sequence, the ligand on high endothelial venules for the lymphocyte homing receptor, L-selectin. Details of the sequences of four other glycan antigens on the podocalyxin are re-evaluated and ambiguities resolved. Regulation of biosynthesis and possible involvements of these glycans in podocalyxin-signaling in stem cells are discussed.

G

  1. Gao, Chao

    1. Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Open Access
      Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Nian Wu, Lisete M. Silva, Yan Liu, Yibing Zhang, Chao Gao, Fuming Zhang, Li Fu, Yanfei Peng, Robert Linhardt, Toshisuke Kawasaki, Barbara Mulloy, Wengang Chai and Ten Feizi
      Molecular & Cellular Proteomics October 1, 2019, First published on July 15, 2019, 18 (10) 1981-2002; https://doi.org/10.1074/mcp.RA119.001309

      R-10G antigen of human iPS and ES cells has been assigned as a unique mono-sulfated glycan. We highlight its relationship to a known bioactive glycan sequence, the ligand on high endothelial venules for the lymphocyte homing receptor, L-selectin. Details of the sequences of four other glycan antigens on the podocalyxin are re-evaluated and ambiguities resolved. Regulation of biosynthesis and possible involvements of these glycans in podocalyxin-signaling in stem cells are discussed.

  2. García, Carlos

    1. Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      You have access
      Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      Patricia Fernández-Puente, Lucía González-Rodríguez, Valentina Calamia, Florencia Picchi, Lucía Lourido, María Camacho-Encina, Natividad Oreiro, Beatriz Rocha, Rocío Paz-González, Anabel Marina, Carlos García, Francisco J. Blanco and Cristina Ruiz-Romero
      Molecular & Cellular Proteomics October 1, 2019, First published on July 27, 2019, 18 (10) 2018-2028; https://doi.org/10.1074/mcp.RA119.001554

      Osteoarthritis (OA) is a disease primarily characterized by the loss of cartilage extracellular matrix. We have followed a peptidomic strategy to identify endogenous peptides (neopeptides) released from healthy and OA human knee and hip articular cartilage, which may serve as disease markers. This study provides a comprehensive neopeptidomic profile of healthy and diseased tissues, and the identification and validation of a panel of eight endogenous peptides that are differentially released from the extracellular matrix because of the pathogenic process.

  3. González-Rodríguez, Lucía

    1. Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      You have access
      Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      Patricia Fernández-Puente, Lucía González-Rodríguez, Valentina Calamia, Florencia Picchi, Lucía Lourido, María Camacho-Encina, Natividad Oreiro, Beatriz Rocha, Rocío Paz-González, Anabel Marina, Carlos García, Francisco J. Blanco and Cristina Ruiz-Romero
      Molecular & Cellular Proteomics October 1, 2019, First published on July 27, 2019, 18 (10) 2018-2028; https://doi.org/10.1074/mcp.RA119.001554

      Osteoarthritis (OA) is a disease primarily characterized by the loss of cartilage extracellular matrix. We have followed a peptidomic strategy to identify endogenous peptides (neopeptides) released from healthy and OA human knee and hip articular cartilage, which may serve as disease markers. This study provides a comprehensive neopeptidomic profile of healthy and diseased tissues, and the identification and validation of a panel of eight endogenous peptides that are differentially released from the extracellular matrix because of the pathogenic process.

  4. Goswami, Neha

    1. A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      You have access
      A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      Anja M. Billing, Shaima S. Dib, Aditya M. Bhagwat, Israel T. da Silva, Rodrigo D. Drummond, Shahina Hayat, Rasha Al-Mismar, Hisham Ben-Hamidane, Neha Goswami, Kasper Engholm-Keller, Martin R. Larsen, Karsten Suhre, Arash Rafii and Johannes Graumann
      Molecular & Cellular Proteomics October 1, 2019, First published on July 22, 2019, 18 (10) 1950-1966; https://doi.org/10.1074/mcp.RA119.001356

      In this integrative, multi-omics study we characterized the differentiation of human embryonic stem cells into mesenchymal stem cells using transcriptomics, quantitative MS-based proteomics and phosphoproteomics. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation with AHNAK hypothesized to be a defining factor in MSC biology. Additional central findings include two distinct expression waves of developmental HOX genes as well as an AGO2-to-AGO3 switch in gene silencing.

  5. Graumann, Johannes

    1. A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      You have access
      A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      Anja M. Billing, Shaima S. Dib, Aditya M. Bhagwat, Israel T. da Silva, Rodrigo D. Drummond, Shahina Hayat, Rasha Al-Mismar, Hisham Ben-Hamidane, Neha Goswami, Kasper Engholm-Keller, Martin R. Larsen, Karsten Suhre, Arash Rafii and Johannes Graumann
      Molecular & Cellular Proteomics October 1, 2019, First published on July 22, 2019, 18 (10) 1950-1966; https://doi.org/10.1074/mcp.RA119.001356

      In this integrative, multi-omics study we characterized the differentiation of human embryonic stem cells into mesenchymal stem cells using transcriptomics, quantitative MS-based proteomics and phosphoproteomics. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation with AHNAK hypothesized to be a defining factor in MSC biology. Additional central findings include two distinct expression waves of developmental HOX genes as well as an AGO2-to-AGO3 switch in gene silencing.

  6. Gu, Po-Wen

    1. Proteomic Profiling of Paired Interstitial Fluids Reveals Dysregulated Pathways and Salivary NID1 as a Biomarker of Oral Cavity Squamous Cell Carcinoma
      You have access
      Proteomic Profiling of Paired Interstitial Fluids Reveals Dysregulated Pathways and Salivary NID1 as a Biomarker of Oral Cavity Squamous Cell Carcinoma
      Chia-Wei Hsu, Kai-Ping Chang, Yenlin Huang, Hao-Ping Liu, Pei-Chun Hsueh, Po-Wen Gu, Wei-Chen Yen and Chih-Ching Wu
      Molecular & Cellular Proteomics October 1, 2019, First published on July 17, 2019, 18 (10) 1939-1949; https://doi.org/10.1074/mcp.RA119.001654

      Oral cavity squamous cell carcinoma (OSCC) is frequently diagnosed at an advanced stage, leading to poor prognosis and high mortality rate. To develop method for OSCC detection, proteome of tumor interstitial fluids (TIFs) has been profiled. The proteins differentially expressed in TIFs were highly associated with aminoacyl tRNA biosynthesis pathway. Importantly, nidogen-1 is a potential diagnostic and/or prognostic biomarker. The results suggest that TIF analysis facilitates understanding of OSCC microenvironment and discovery of biomarker candidates.

  7. Guan, Shenheng

    1. Prediction of LC-MS/MS Properties of Peptides from Sequence by Deep Learning
      Open Access
      Prediction of LC-MS/MS Properties of Peptides from Sequence by Deep Learning
      Shenheng Guan, Michael F. Moran and Bin Ma
      Molecular & Cellular Proteomics October 1, 2019, First published on June 27, 2019, 18 (10) 2099-2107; https://doi.org/10.1074/mcp.TIR119.001412

      Indexed retention times (iRT), MS1 (the first level of mass analysis) or survey scan charge state distributions, and sequence ion intensities of MSMS (tandom mass spectrometry) spectra were predicted from peptide sequence by use of long-short term memory (LSTM) recurrent neural networks models. Data points on the order of 105 were used to train the iRT and charge state distribution models. An HCD sequence ion prediction model was trained with 2×106 experimental spectra. The models with a simple deep learning architecture can predict those three key LC-MS/MS (Liquid chromatography-tandem mass spectrometry) properties with superior accuracies.

  8. Gupta, Meera

    1. Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-statistics with Peptide Quantification Concordance
      You have access
      Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-statistics with Peptide Quantification Concordance
      Leonid Peshkin, Meera Gupta, Lillia Ryazanova and Martin Wühr
      Molecular & Cellular Proteomics October 1, 2019, First published on July 16, 2019, 18 (10) 2108-2120; https://doi.org/10.1074/mcp.TIR119.001317

      Multiplexed proteomics has become a powerful tool to assay biological systems. So far, the data is typically interpreted via naive peptide averaging. Here, we present a Bayesian approach that integrates peptide quantification concordance and ion statistics into the most probable answer with confidence intervals. Our approach considers low signal peptides, does not require replicates, and detects smaller significant changes than alternative approaches. Thus, our method increases the value of proteomics experiments, helping researchers to interpret data and prioritize resources.

H

  1. Hayat, Shahina

    1. A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      You have access
      A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      Anja M. Billing, Shaima S. Dib, Aditya M. Bhagwat, Israel T. da Silva, Rodrigo D. Drummond, Shahina Hayat, Rasha Al-Mismar, Hisham Ben-Hamidane, Neha Goswami, Kasper Engholm-Keller, Martin R. Larsen, Karsten Suhre, Arash Rafii and Johannes Graumann
      Molecular & Cellular Proteomics October 1, 2019, First published on July 22, 2019, 18 (10) 1950-1966; https://doi.org/10.1074/mcp.RA119.001356

      In this integrative, multi-omics study we characterized the differentiation of human embryonic stem cells into mesenchymal stem cells using transcriptomics, quantitative MS-based proteomics and phosphoproteomics. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation with AHNAK hypothesized to be a defining factor in MSC biology. Additional central findings include two distinct expression waves of developmental HOX genes as well as an AGO2-to-AGO3 switch in gene silencing.

  2. Hsu, Chia-Wei

    1. Proteomic Profiling of Paired Interstitial Fluids Reveals Dysregulated Pathways and Salivary NID1 as a Biomarker of Oral Cavity Squamous Cell Carcinoma
      You have access
      Proteomic Profiling of Paired Interstitial Fluids Reveals Dysregulated Pathways and Salivary NID1 as a Biomarker of Oral Cavity Squamous Cell Carcinoma
      Chia-Wei Hsu, Kai-Ping Chang, Yenlin Huang, Hao-Ping Liu, Pei-Chun Hsueh, Po-Wen Gu, Wei-Chen Yen and Chih-Ching Wu
      Molecular & Cellular Proteomics October 1, 2019, First published on July 17, 2019, 18 (10) 1939-1949; https://doi.org/10.1074/mcp.RA119.001654

      Oral cavity squamous cell carcinoma (OSCC) is frequently diagnosed at an advanced stage, leading to poor prognosis and high mortality rate. To develop method for OSCC detection, proteome of tumor interstitial fluids (TIFs) has been profiled. The proteins differentially expressed in TIFs were highly associated with aminoacyl tRNA biosynthesis pathway. Importantly, nidogen-1 is a potential diagnostic and/or prognostic biomarker. The results suggest that TIF analysis facilitates understanding of OSCC microenvironment and discovery of biomarker candidates.

  3. Hsueh, Pei-Chun

    1. Proteomic Profiling of Paired Interstitial Fluids Reveals Dysregulated Pathways and Salivary NID1 as a Biomarker of Oral Cavity Squamous Cell Carcinoma
      You have access
      Proteomic Profiling of Paired Interstitial Fluids Reveals Dysregulated Pathways and Salivary NID1 as a Biomarker of Oral Cavity Squamous Cell Carcinoma
      Chia-Wei Hsu, Kai-Ping Chang, Yenlin Huang, Hao-Ping Liu, Pei-Chun Hsueh, Po-Wen Gu, Wei-Chen Yen and Chih-Ching Wu
      Molecular & Cellular Proteomics October 1, 2019, First published on July 17, 2019, 18 (10) 1939-1949; https://doi.org/10.1074/mcp.RA119.001654

      Oral cavity squamous cell carcinoma (OSCC) is frequently diagnosed at an advanced stage, leading to poor prognosis and high mortality rate. To develop method for OSCC detection, proteome of tumor interstitial fluids (TIFs) has been profiled. The proteins differentially expressed in TIFs were highly associated with aminoacyl tRNA biosynthesis pathway. Importantly, nidogen-1 is a potential diagnostic and/or prognostic biomarker. The results suggest that TIF analysis facilitates understanding of OSCC microenvironment and discovery of biomarker candidates.

  4. Huang, Yenlin

    1. Proteomic Profiling of Paired Interstitial Fluids Reveals Dysregulated Pathways and Salivary NID1 as a Biomarker of Oral Cavity Squamous Cell Carcinoma
      You have access
      Proteomic Profiling of Paired Interstitial Fluids Reveals Dysregulated Pathways and Salivary NID1 as a Biomarker of Oral Cavity Squamous Cell Carcinoma
      Chia-Wei Hsu, Kai-Ping Chang, Yenlin Huang, Hao-Ping Liu, Pei-Chun Hsueh, Po-Wen Gu, Wei-Chen Yen and Chih-Ching Wu
      Molecular & Cellular Proteomics October 1, 2019, First published on July 17, 2019, 18 (10) 1939-1949; https://doi.org/10.1074/mcp.RA119.001654

      Oral cavity squamous cell carcinoma (OSCC) is frequently diagnosed at an advanced stage, leading to poor prognosis and high mortality rate. To develop method for OSCC detection, proteome of tumor interstitial fluids (TIFs) has been profiled. The proteins differentially expressed in TIFs were highly associated with aminoacyl tRNA biosynthesis pathway. Importantly, nidogen-1 is a potential diagnostic and/or prognostic biomarker. The results suggest that TIF analysis facilitates understanding of OSCC microenvironment and discovery of biomarker candidates.

  5. Hukelmann, Jens

    1. Multibatch TMT Reveals False Positives, Batch Effects and Missing Values
      Open Access
      Multibatch TMT Reveals False Positives, Batch Effects and Missing Values
      Alejandro Brenes, Jens Hukelmann, Dalila Bensaddek and Angus I. Lamond
      Molecular & Cellular Proteomics October 1, 2019, First published on July 22, 2019, 18 (10) 1967-1980; https://doi.org/10.1074/mcp.RA119.001472

      Analysis of 24 TMT 10-plex batches revealed an inflation in missing values and reduced inter-batch accuracy as multiple TMT batches are integrated. Our data also highlights the incidence of false positives exemplified by Y chromosome peptides being detected in female channels. The Y chromosome peptides were then used to quantify the effects of coisolation and reporter ion interference on TMT quantification and to propose an experimental design that would minimise cross population reporter ion interference.

J

  1. Jaffe, Jacob D.

    1. Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS
      You have access
      Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS
      Malvina Papanastasiou, James Mullahoo, Katherine C. DeRuff, Besnik Bajrami, Ioannis Karageorgos, Stephen E. Johnston, Ryan Peckner, Samuel A. Myers, Steven A. Carr and Jacob D. Jaffe
      Molecular & Cellular Proteomics October 1, 2019, First published on August 13, 2019, 18 (10) 2089-2098; https://doi.org/10.1074/mcp.RA119.001325

      Cathepsin-L, a protease known to proteolyse histone tails in cells, is introduced as a novel enzyme for HX-MS. Cathepsin-L generates overlapping N-terminal peptides, improving coverage of histone tails that are poorly represented in HX-MS employing pepsin alone. Cathepsin-L/pepsin is employed to investigate in-solution dynamics of H3 and H4 monomers. Rapid deuteration of the tails is indicative of unfolded polypeptides, whereas extensive bimodal distributions detected in the histone-folds reveal cooperative unfolding events.

  2. Jeffs, Joshua W.

    1. Delta-S-Cys-Albumin: A Lab Test that Quantifies Cumulative Exposure of Archived Human Blood Plasma and Serum Samples to Thawed Conditions
      Open Access
      Delta-S-Cys-Albumin: A Lab Test that Quantifies Cumulative Exposure of Archived Human Blood Plasma and Serum Samples to Thawed Conditions
      Joshua W. Jeffs, Nilojan Jehanathan, Stephanie M. F. Thibert, Shadi Ferdosi, Linda Pham, Zachary T. Wilson, Christian Breburda and Chad R. Borges
      Molecular & Cellular Proteomics October 1, 2019, First published on July 19, 2019, 18 (10) 2121-2137; https://doi.org/10.1074/mcp.TIR119.001659

      ΔS-Cys-Albumin, an endogenous marker of plasma and serum (P/S) exposure to thawed conditions (> −30 °C) based on the ex vivo S-cysteinylation (oxidizability) of albumin was developed. Average values in fresh P/S samples from a population of nonacute cardiac patients were determined. The multireaction mechanism that drives changes in albumin S-cysteinylation is known and the rate law for it has been established and accurately modeled in P/S. Measurement of ΔS-Cys-Albumin in unknown samples facilitates estimation of thawed-state exposure times.

  3. Jehanathan, Nilojan

    1. Delta-S-Cys-Albumin: A Lab Test that Quantifies Cumulative Exposure of Archived Human Blood Plasma and Serum Samples to Thawed Conditions
      Open Access
      Delta-S-Cys-Albumin: A Lab Test that Quantifies Cumulative Exposure of Archived Human Blood Plasma and Serum Samples to Thawed Conditions
      Joshua W. Jeffs, Nilojan Jehanathan, Stephanie M. F. Thibert, Shadi Ferdosi, Linda Pham, Zachary T. Wilson, Christian Breburda and Chad R. Borges
      Molecular & Cellular Proteomics October 1, 2019, First published on July 19, 2019, 18 (10) 2121-2137; https://doi.org/10.1074/mcp.TIR119.001659

      ΔS-Cys-Albumin, an endogenous marker of plasma and serum (P/S) exposure to thawed conditions (> −30 °C) based on the ex vivo S-cysteinylation (oxidizability) of albumin was developed. Average values in fresh P/S samples from a population of nonacute cardiac patients were determined. The multireaction mechanism that drives changes in albumin S-cysteinylation is known and the rate law for it has been established and accurately modeled in P/S. Measurement of ΔS-Cys-Albumin in unknown samples facilitates estimation of thawed-state exposure times.

  4. Jevtic, Stefan

    1. Defining Protein Pattern Differences Among Molecular Subtypes of Diffuse Gliomas Using Mass Spectrometry
      You have access
      Defining Protein Pattern Differences Among Molecular Subtypes of Diffuse Gliomas Using Mass Spectrometry
      Ugljesa Djuric, K. H. Brian Lam, Jennifer Kao, Ihor Batruch, Stefan Jevtic, Michail-Dimitrios Papaioannou and Phedias Diamandis
      Molecular & Cellular Proteomics October 1, 2019, First published on July 28, 2019, 18 (10) 2029-2043; https://doi.org/10.1074/mcp.RA119.001521

      Gliomas represent the most common brain tumor type. Molecular and global omics are becoming powerful tools for tumor subclassification that will facilitate more subtype-specific treatment options for patients. Here, we demonstrate that proteomic-based subclassification of closely related gliomas, differentiated by IDH mutation and 1p19q chromosome codeletion status, is facilitated by tumor microdissections prior to mass spectrometry analysis. Identified protein modules are confirmed in tissue culture grown glioma stem cells and point to chloride transport and stress proteins as strong drivers of glioma molecular diversions.

  5. Johnston, Stephen E.

    1. Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS
      You have access
      Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS
      Malvina Papanastasiou, James Mullahoo, Katherine C. DeRuff, Besnik Bajrami, Ioannis Karageorgos, Stephen E. Johnston, Ryan Peckner, Samuel A. Myers, Steven A. Carr and Jacob D. Jaffe
      Molecular & Cellular Proteomics October 1, 2019, First published on August 13, 2019, 18 (10) 2089-2098; https://doi.org/10.1074/mcp.RA119.001325

      Cathepsin-L, a protease known to proteolyse histone tails in cells, is introduced as a novel enzyme for HX-MS. Cathepsin-L generates overlapping N-terminal peptides, improving coverage of histone tails that are poorly represented in HX-MS employing pepsin alone. Cathepsin-L/pepsin is employed to investigate in-solution dynamics of H3 and H4 monomers. Rapid deuteration of the tails is indicative of unfolded polypeptides, whereas extensive bimodal distributions detected in the histone-folds reveal cooperative unfolding events.

K

  1. Kao, Jennifer

    1. Defining Protein Pattern Differences Among Molecular Subtypes of Diffuse Gliomas Using Mass Spectrometry
      You have access
      Defining Protein Pattern Differences Among Molecular Subtypes of Diffuse Gliomas Using Mass Spectrometry
      Ugljesa Djuric, K. H. Brian Lam, Jennifer Kao, Ihor Batruch, Stefan Jevtic, Michail-Dimitrios Papaioannou and Phedias Diamandis
      Molecular & Cellular Proteomics October 1, 2019, First published on July 28, 2019, 18 (10) 2029-2043; https://doi.org/10.1074/mcp.RA119.001521

      Gliomas represent the most common brain tumor type. Molecular and global omics are becoming powerful tools for tumor subclassification that will facilitate more subtype-specific treatment options for patients. Here, we demonstrate that proteomic-based subclassification of closely related gliomas, differentiated by IDH mutation and 1p19q chromosome codeletion status, is facilitated by tumor microdissections prior to mass spectrometry analysis. Identified protein modules are confirmed in tissue culture grown glioma stem cells and point to chloride transport and stress proteins as strong drivers of glioma molecular diversions.

  2. Karageorgos, Ioannis

    1. Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS
      You have access
      Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS
      Malvina Papanastasiou, James Mullahoo, Katherine C. DeRuff, Besnik Bajrami, Ioannis Karageorgos, Stephen E. Johnston, Ryan Peckner, Samuel A. Myers, Steven A. Carr and Jacob D. Jaffe
      Molecular & Cellular Proteomics October 1, 2019, First published on August 13, 2019, 18 (10) 2089-2098; https://doi.org/10.1074/mcp.RA119.001325

      Cathepsin-L, a protease known to proteolyse histone tails in cells, is introduced as a novel enzyme for HX-MS. Cathepsin-L generates overlapping N-terminal peptides, improving coverage of histone tails that are poorly represented in HX-MS employing pepsin alone. Cathepsin-L/pepsin is employed to investigate in-solution dynamics of H3 and H4 monomers. Rapid deuteration of the tails is indicative of unfolded polypeptides, whereas extensive bimodal distributions detected in the histone-folds reveal cooperative unfolding events.

  3. Kawasaki, Toshisuke

    1. Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Open Access
      Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Nian Wu, Lisete M. Silva, Yan Liu, Yibing Zhang, Chao Gao, Fuming Zhang, Li Fu, Yanfei Peng, Robert Linhardt, Toshisuke Kawasaki, Barbara Mulloy, Wengang Chai and Ten Feizi
      Molecular & Cellular Proteomics October 1, 2019, First published on July 15, 2019, 18 (10) 1981-2002; https://doi.org/10.1074/mcp.RA119.001309

      R-10G antigen of human iPS and ES cells has been assigned as a unique mono-sulfated glycan. We highlight its relationship to a known bioactive glycan sequence, the ligand on high endothelial venules for the lymphocyte homing receptor, L-selectin. Details of the sequences of four other glycan antigens on the podocalyxin are re-evaluated and ambiguities resolved. Regulation of biosynthesis and possible involvements of these glycans in podocalyxin-signaling in stem cells are discussed.

  4. Kizuka, Yasuhiko

    1. Bisecting GlcNAc Is a General Suppressor of Terminal Modification of <em>N</em>-glycan
      You have access
      Bisecting GlcNAc Is a General Suppressor of Terminal Modification of N-glycan
      Miyako Nakano, Sushil K. Mishra, Yuko Tokoro, Keiko Sato, Kazuki Nakajima, Yoshiki Yamaguchi, Naoyuki Taniguchi and Yasuhiko Kizuka
      Molecular & Cellular Proteomics October 1, 2019, First published on August 2, 2019, 18 (10) 2044-2057; https://doi.org/10.1074/mcp.RA119.001534

      Bisecting GlcNAc, a branching sugar in N-glycan highly expressed in brain, is involved in Alzheimer's disease, but its physiological function is largely unclear. In this manuscript, the authors revealed that loss of bisecting GlcNAc in mice leads to upregulation of various types of terminal modifications of N-glycans. As a mechanism, many glycosyltransferases were found to commonly prefer glycans without bisecting GlcNAc as a substrate. These data indicate that bisecting GlcNAc generally suppresses terminal modifications of N-glycans.

  5. Krzystyniak, Adam

    1. Stress-induced Changes in the S-palmitoylation and S-nitrosylation of Synaptic Proteins
      You have access
      Stress-induced Changes in the S-palmitoylation and S-nitrosylation of Synaptic Proteins
      Monika Zareba-Koziol, Anna Bartkowiak-Kaczmarek, Izabela Figiel, Adam Krzystyniak, Tomasz Wojtowicz, Monika Bijata and Jakub Wlodarczyk
      Molecular & Cellular Proteomics October 1, 2019, First published on July 16, 2019, 18 (10) 1916-1938; https://doi.org/10.1074/mcp.RA119.001581

      To improve simultaneous S-palmitoylation and S-nitrosylation site profiling, we developed a novel mass spectrometry-based strategy Palmitoylation And Nitrosylation Interplay Monitoring (PANIMoni). Using this approach we evaluated dynamic, site-specific changes in two important cysteine modifications, S-PALM and S-NO, in a mouse model of chronic stress. High-throughput analysis provided valuable insight into chronic, stress-induced remodeling of the synaptic proteome. Based on the obtained data, we postulate that the mechanism underlying chronic stress involves mutual competition between S-PALM and S-NO for modification sites.

L

  1. Lam, K. H. Brian

    1. Defining Protein Pattern Differences Among Molecular Subtypes of Diffuse Gliomas Using Mass Spectrometry
      You have access
      Defining Protein Pattern Differences Among Molecular Subtypes of Diffuse Gliomas Using Mass Spectrometry
      Ugljesa Djuric, K. H. Brian Lam, Jennifer Kao, Ihor Batruch, Stefan Jevtic, Michail-Dimitrios Papaioannou and Phedias Diamandis
      Molecular & Cellular Proteomics October 1, 2019, First published on July 28, 2019, 18 (10) 2029-2043; https://doi.org/10.1074/mcp.RA119.001521

      Gliomas represent the most common brain tumor type. Molecular and global omics are becoming powerful tools for tumor subclassification that will facilitate more subtype-specific treatment options for patients. Here, we demonstrate that proteomic-based subclassification of closely related gliomas, differentiated by IDH mutation and 1p19q chromosome codeletion status, is facilitated by tumor microdissections prior to mass spectrometry analysis. Identified protein modules are confirmed in tissue culture grown glioma stem cells and point to chloride transport and stress proteins as strong drivers of glioma molecular diversions.

  2. Lamond, Angus I.

    1. Multibatch TMT Reveals False Positives, Batch Effects and Missing Values
      Open Access
      Multibatch TMT Reveals False Positives, Batch Effects and Missing Values
      Alejandro Brenes, Jens Hukelmann, Dalila Bensaddek and Angus I. Lamond
      Molecular & Cellular Proteomics October 1, 2019, First published on July 22, 2019, 18 (10) 1967-1980; https://doi.org/10.1074/mcp.RA119.001472

      Analysis of 24 TMT 10-plex batches revealed an inflation in missing values and reduced inter-batch accuracy as multiple TMT batches are integrated. Our data also highlights the incidence of false positives exemplified by Y chromosome peptides being detected in female channels. The Y chromosome peptides were then used to quantify the effects of coisolation and reporter ion interference on TMT quantification and to propose an experimental design that would minimise cross population reporter ion interference.

  3. Larsen, Martin R.

    1. A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      You have access
      A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      Anja M. Billing, Shaima S. Dib, Aditya M. Bhagwat, Israel T. da Silva, Rodrigo D. Drummond, Shahina Hayat, Rasha Al-Mismar, Hisham Ben-Hamidane, Neha Goswami, Kasper Engholm-Keller, Martin R. Larsen, Karsten Suhre, Arash Rafii and Johannes Graumann
      Molecular & Cellular Proteomics October 1, 2019, First published on July 22, 2019, 18 (10) 1950-1966; https://doi.org/10.1074/mcp.RA119.001356

      In this integrative, multi-omics study we characterized the differentiation of human embryonic stem cells into mesenchymal stem cells using transcriptomics, quantitative MS-based proteomics and phosphoproteomics. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation with AHNAK hypothesized to be a defining factor in MSC biology. Additional central findings include two distinct expression waves of developmental HOX genes as well as an AGO2-to-AGO3 switch in gene silencing.

  4. Li, Peng

    1. <em>Sc</em>CobB2-mediated Lysine Desuccinylation Regulates Protein Biosynthesis and Carbon Metabolism in <em>Streptomyces coelicolor</em>
      You have access
      ScCobB2-mediated Lysine Desuccinylation Regulates Protein Biosynthesis and Carbon Metabolism in Streptomyces coelicolor
      Hong Zhang, Peng Li, Shuangxi Ren, Zhongyi Cheng, Guoping Zhao and Wei Zhao
      Molecular & Cellular Proteomics October 1, 2019, First published on July 23, 2019, 18 (10) 2003-2017; https://doi.org/10.1074/mcp.RA118.001298

      Lysine succinylation is a prevalent protein modification that regulates multiple critical cellular processes. Here, we performed a quantitative succinylome analysis in the model soil bacterium Streptomyces coelicolor after characterization of a specific desuccinylase ScCobB2. Comparison of the ΔScCobB2 to the wild-type succinylome identified a total of 673 unique succinylated sites, and among which, 144 protein sites are statistically hypersuccinylated in ΔScCobB2 cells. Analyses of these hypersuccinylated proteins suggested they are enriched in two major pathways, protein biosynthesis and carbon metabolism. We propose that ScCobB2 has critical regulatory roles in S. coelicolor cellular physiology.

  5. Linhardt, Robert

    1. Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Open Access
      Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Nian Wu, Lisete M. Silva, Yan Liu, Yibing Zhang, Chao Gao, Fuming Zhang, Li Fu, Yanfei Peng, Robert Linhardt, Toshisuke Kawasaki, Barbara Mulloy, Wengang Chai and Ten Feizi
      Molecular & Cellular Proteomics October 1, 2019, First published on July 15, 2019, 18 (10) 1981-2002; https://doi.org/10.1074/mcp.RA119.001309

      R-10G antigen of human iPS and ES cells has been assigned as a unique mono-sulfated glycan. We highlight its relationship to a known bioactive glycan sequence, the ligand on high endothelial venules for the lymphocyte homing receptor, L-selectin. Details of the sequences of four other glycan antigens on the podocalyxin are re-evaluated and ambiguities resolved. Regulation of biosynthesis and possible involvements of these glycans in podocalyxin-signaling in stem cells are discussed.

  6. Liu, Hao-Ping

    1. Proteomic Profiling of Paired Interstitial Fluids Reveals Dysregulated Pathways and Salivary NID1 as a Biomarker of Oral Cavity Squamous Cell Carcinoma
      You have access
      Proteomic Profiling of Paired Interstitial Fluids Reveals Dysregulated Pathways and Salivary NID1 as a Biomarker of Oral Cavity Squamous Cell Carcinoma
      Chia-Wei Hsu, Kai-Ping Chang, Yenlin Huang, Hao-Ping Liu, Pei-Chun Hsueh, Po-Wen Gu, Wei-Chen Yen and Chih-Ching Wu
      Molecular & Cellular Proteomics October 1, 2019, First published on July 17, 2019, 18 (10) 1939-1949; https://doi.org/10.1074/mcp.RA119.001654

      Oral cavity squamous cell carcinoma (OSCC) is frequently diagnosed at an advanced stage, leading to poor prognosis and high mortality rate. To develop method for OSCC detection, proteome of tumor interstitial fluids (TIFs) has been profiled. The proteins differentially expressed in TIFs were highly associated with aminoacyl tRNA biosynthesis pathway. Importantly, nidogen-1 is a potential diagnostic and/or prognostic biomarker. The results suggest that TIF analysis facilitates understanding of OSCC microenvironment and discovery of biomarker candidates.

  7. Liu, Nan

    1. Multidimensional Proteomics Identifies Declines in Protein Homeostasis and Mitochondria as Early Signals for Normal Aging and Age-associated Disease in <em>Drosophila</em>
      You have access
      Multidimensional Proteomics Identifies Declines in Protein Homeostasis and Mitochondria as Early Signals for Normal Aging and Age-associated Disease in Drosophila
      Lu Yang, Ye Cao, Jing Zhao, Yanshan Fang, Nan Liu and Yaoyang Zhang
      Molecular & Cellular Proteomics October 1, 2019, First published on August 21, 2019, 18 (10) 2078-2088; https://doi.org/10.1074/mcp.RA119.001621

      Yang et al. have profiled the snapshot and dynamics of the proteomes from Drosophila somatic and reproductive tissues during aging, revealing both tissue-specific and common pathways that are modulated with age. Analysis of proteome dynamics demonstrates that the global protein synthesis, particularly for those proteins functionally related to proteostasis and mitochondria, is down-regulated during normal aging, and that this decline becomes dramatically enhanced in the Drosophila model of human Parkinson's disease.

  8. Liu, Yan

    1. Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Open Access
      Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Nian Wu, Lisete M. Silva, Yan Liu, Yibing Zhang, Chao Gao, Fuming Zhang, Li Fu, Yanfei Peng, Robert Linhardt, Toshisuke Kawasaki, Barbara Mulloy, Wengang Chai and Ten Feizi
      Molecular & Cellular Proteomics October 1, 2019, First published on July 15, 2019, 18 (10) 1981-2002; https://doi.org/10.1074/mcp.RA119.001309

      R-10G antigen of human iPS and ES cells has been assigned as a unique mono-sulfated glycan. We highlight its relationship to a known bioactive glycan sequence, the ligand on high endothelial venules for the lymphocyte homing receptor, L-selectin. Details of the sequences of four other glycan antigens on the podocalyxin are re-evaluated and ambiguities resolved. Regulation of biosynthesis and possible involvements of these glycans in podocalyxin-signaling in stem cells are discussed.

  9. Lourido, Lucía

    1. Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      You have access
      Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      Patricia Fernández-Puente, Lucía González-Rodríguez, Valentina Calamia, Florencia Picchi, Lucía Lourido, María Camacho-Encina, Natividad Oreiro, Beatriz Rocha, Rocío Paz-González, Anabel Marina, Carlos García, Francisco J. Blanco and Cristina Ruiz-Romero
      Molecular & Cellular Proteomics October 1, 2019, First published on July 27, 2019, 18 (10) 2018-2028; https://doi.org/10.1074/mcp.RA119.001554

      Osteoarthritis (OA) is a disease primarily characterized by the loss of cartilage extracellular matrix. We have followed a peptidomic strategy to identify endogenous peptides (neopeptides) released from healthy and OA human knee and hip articular cartilage, which may serve as disease markers. This study provides a comprehensive neopeptidomic profile of healthy and diseased tissues, and the identification and validation of a panel of eight endogenous peptides that are differentially released from the extracellular matrix because of the pathogenic process.

M

  1. Ma, Bin

    1. Prediction of LC-MS/MS Properties of Peptides from Sequence by Deep Learning
      Open Access
      Prediction of LC-MS/MS Properties of Peptides from Sequence by Deep Learning
      Shenheng Guan, Michael F. Moran and Bin Ma
      Molecular & Cellular Proteomics October 1, 2019, First published on June 27, 2019, 18 (10) 2099-2107; https://doi.org/10.1074/mcp.TIR119.001412

      Indexed retention times (iRT), MS1 (the first level of mass analysis) or survey scan charge state distributions, and sequence ion intensities of MSMS (tandom mass spectrometry) spectra were predicted from peptide sequence by use of long-short term memory (LSTM) recurrent neural networks models. Data points on the order of 105 were used to train the iRT and charge state distribution models. An HCD sequence ion prediction model was trained with 2×106 experimental spectra. The models with a simple deep learning architecture can predict those three key LC-MS/MS (Liquid chromatography-tandem mass spectrometry) properties with superior accuracies.

  2. Marina, Anabel

    1. Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      You have access
      Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      Patricia Fernández-Puente, Lucía González-Rodríguez, Valentina Calamia, Florencia Picchi, Lucía Lourido, María Camacho-Encina, Natividad Oreiro, Beatriz Rocha, Rocío Paz-González, Anabel Marina, Carlos García, Francisco J. Blanco and Cristina Ruiz-Romero
      Molecular & Cellular Proteomics October 1, 2019, First published on July 27, 2019, 18 (10) 2018-2028; https://doi.org/10.1074/mcp.RA119.001554

      Osteoarthritis (OA) is a disease primarily characterized by the loss of cartilage extracellular matrix. We have followed a peptidomic strategy to identify endogenous peptides (neopeptides) released from healthy and OA human knee and hip articular cartilage, which may serve as disease markers. This study provides a comprehensive neopeptidomic profile of healthy and diseased tissues, and the identification and validation of a panel of eight endogenous peptides that are differentially released from the extracellular matrix because of the pathogenic process.

  3. Mishra, Sushil K.

    1. Bisecting GlcNAc Is a General Suppressor of Terminal Modification of <em>N</em>-glycan
      You have access
      Bisecting GlcNAc Is a General Suppressor of Terminal Modification of N-glycan
      Miyako Nakano, Sushil K. Mishra, Yuko Tokoro, Keiko Sato, Kazuki Nakajima, Yoshiki Yamaguchi, Naoyuki Taniguchi and Yasuhiko Kizuka
      Molecular & Cellular Proteomics October 1, 2019, First published on August 2, 2019, 18 (10) 2044-2057; https://doi.org/10.1074/mcp.RA119.001534

      Bisecting GlcNAc, a branching sugar in N-glycan highly expressed in brain, is involved in Alzheimer's disease, but its physiological function is largely unclear. In this manuscript, the authors revealed that loss of bisecting GlcNAc in mice leads to upregulation of various types of terminal modifications of N-glycans. As a mechanism, many glycosyltransferases were found to commonly prefer glycans without bisecting GlcNAc as a substrate. These data indicate that bisecting GlcNAc generally suppresses terminal modifications of N-glycans.

  4. Moran, Michael F.

    1. Prediction of LC-MS/MS Properties of Peptides from Sequence by Deep Learning
      Open Access
      Prediction of LC-MS/MS Properties of Peptides from Sequence by Deep Learning
      Shenheng Guan, Michael F. Moran and Bin Ma
      Molecular & Cellular Proteomics October 1, 2019, First published on June 27, 2019, 18 (10) 2099-2107; https://doi.org/10.1074/mcp.TIR119.001412

      Indexed retention times (iRT), MS1 (the first level of mass analysis) or survey scan charge state distributions, and sequence ion intensities of MSMS (tandom mass spectrometry) spectra were predicted from peptide sequence by use of long-short term memory (LSTM) recurrent neural networks models. Data points on the order of 105 were used to train the iRT and charge state distribution models. An HCD sequence ion prediction model was trained with 2×106 experimental spectra. The models with a simple deep learning architecture can predict those three key LC-MS/MS (Liquid chromatography-tandem mass spectrometry) properties with superior accuracies.

  5. Mullahoo, James

    1. Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS
      You have access
      Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS
      Malvina Papanastasiou, James Mullahoo, Katherine C. DeRuff, Besnik Bajrami, Ioannis Karageorgos, Stephen E. Johnston, Ryan Peckner, Samuel A. Myers, Steven A. Carr and Jacob D. Jaffe
      Molecular & Cellular Proteomics October 1, 2019, First published on August 13, 2019, 18 (10) 2089-2098; https://doi.org/10.1074/mcp.RA119.001325

      Cathepsin-L, a protease known to proteolyse histone tails in cells, is introduced as a novel enzyme for HX-MS. Cathepsin-L generates overlapping N-terminal peptides, improving coverage of histone tails that are poorly represented in HX-MS employing pepsin alone. Cathepsin-L/pepsin is employed to investigate in-solution dynamics of H3 and H4 monomers. Rapid deuteration of the tails is indicative of unfolded polypeptides, whereas extensive bimodal distributions detected in the histone-folds reveal cooperative unfolding events.

  6. Mulloy, Barbara

    1. Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Open Access
      Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Nian Wu, Lisete M. Silva, Yan Liu, Yibing Zhang, Chao Gao, Fuming Zhang, Li Fu, Yanfei Peng, Robert Linhardt, Toshisuke Kawasaki, Barbara Mulloy, Wengang Chai and Ten Feizi
      Molecular & Cellular Proteomics October 1, 2019, First published on July 15, 2019, 18 (10) 1981-2002; https://doi.org/10.1074/mcp.RA119.001309

      R-10G antigen of human iPS and ES cells has been assigned as a unique mono-sulfated glycan. We highlight its relationship to a known bioactive glycan sequence, the ligand on high endothelial venules for the lymphocyte homing receptor, L-selectin. Details of the sequences of four other glycan antigens on the podocalyxin are re-evaluated and ambiguities resolved. Regulation of biosynthesis and possible involvements of these glycans in podocalyxin-signaling in stem cells are discussed.

  7. Myers, Samuel A.

    1. Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS
      You have access
      Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS
      Malvina Papanastasiou, James Mullahoo, Katherine C. DeRuff, Besnik Bajrami, Ioannis Karageorgos, Stephen E. Johnston, Ryan Peckner, Samuel A. Myers, Steven A. Carr and Jacob D. Jaffe
      Molecular & Cellular Proteomics October 1, 2019, First published on August 13, 2019, 18 (10) 2089-2098; https://doi.org/10.1074/mcp.RA119.001325

      Cathepsin-L, a protease known to proteolyse histone tails in cells, is introduced as a novel enzyme for HX-MS. Cathepsin-L generates overlapping N-terminal peptides, improving coverage of histone tails that are poorly represented in HX-MS employing pepsin alone. Cathepsin-L/pepsin is employed to investigate in-solution dynamics of H3 and H4 monomers. Rapid deuteration of the tails is indicative of unfolded polypeptides, whereas extensive bimodal distributions detected in the histone-folds reveal cooperative unfolding events.

N

  1. Nakajima, Kazuki

    1. Bisecting GlcNAc Is a General Suppressor of Terminal Modification of <em>N</em>-glycan
      You have access
      Bisecting GlcNAc Is a General Suppressor of Terminal Modification of N-glycan
      Miyako Nakano, Sushil K. Mishra, Yuko Tokoro, Keiko Sato, Kazuki Nakajima, Yoshiki Yamaguchi, Naoyuki Taniguchi and Yasuhiko Kizuka
      Molecular & Cellular Proteomics October 1, 2019, First published on August 2, 2019, 18 (10) 2044-2057; https://doi.org/10.1074/mcp.RA119.001534

      Bisecting GlcNAc, a branching sugar in N-glycan highly expressed in brain, is involved in Alzheimer's disease, but its physiological function is largely unclear. In this manuscript, the authors revealed that loss of bisecting GlcNAc in mice leads to upregulation of various types of terminal modifications of N-glycans. As a mechanism, many glycosyltransferases were found to commonly prefer glycans without bisecting GlcNAc as a substrate. These data indicate that bisecting GlcNAc generally suppresses terminal modifications of N-glycans.

  2. Nakano, Miyako

    1. Bisecting GlcNAc Is a General Suppressor of Terminal Modification of <em>N</em>-glycan
      You have access
      Bisecting GlcNAc Is a General Suppressor of Terminal Modification of N-glycan
      Miyako Nakano, Sushil K. Mishra, Yuko Tokoro, Keiko Sato, Kazuki Nakajima, Yoshiki Yamaguchi, Naoyuki Taniguchi and Yasuhiko Kizuka
      Molecular & Cellular Proteomics October 1, 2019, First published on August 2, 2019, 18 (10) 2044-2057; https://doi.org/10.1074/mcp.RA119.001534

      Bisecting GlcNAc, a branching sugar in N-glycan highly expressed in brain, is involved in Alzheimer's disease, but its physiological function is largely unclear. In this manuscript, the authors revealed that loss of bisecting GlcNAc in mice leads to upregulation of various types of terminal modifications of N-glycans. As a mechanism, many glycosyltransferases were found to commonly prefer glycans without bisecting GlcNAc as a substrate. These data indicate that bisecting GlcNAc generally suppresses terminal modifications of N-glycans.

O

  1. Oreiro, Natividad

    1. Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      You have access
      Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      Patricia Fernández-Puente, Lucía González-Rodríguez, Valentina Calamia, Florencia Picchi, Lucía Lourido, María Camacho-Encina, Natividad Oreiro, Beatriz Rocha, Rocío Paz-González, Anabel Marina, Carlos García, Francisco J. Blanco and Cristina Ruiz-Romero
      Molecular & Cellular Proteomics October 1, 2019, First published on July 27, 2019, 18 (10) 2018-2028; https://doi.org/10.1074/mcp.RA119.001554

      Osteoarthritis (OA) is a disease primarily characterized by the loss of cartilage extracellular matrix. We have followed a peptidomic strategy to identify endogenous peptides (neopeptides) released from healthy and OA human knee and hip articular cartilage, which may serve as disease markers. This study provides a comprehensive neopeptidomic profile of healthy and diseased tissues, and the identification and validation of a panel of eight endogenous peptides that are differentially released from the extracellular matrix because of the pathogenic process.

P

  1. Papaioannou, Michail-Dimitrios

    1. Defining Protein Pattern Differences Among Molecular Subtypes of Diffuse Gliomas Using Mass Spectrometry
      You have access
      Defining Protein Pattern Differences Among Molecular Subtypes of Diffuse Gliomas Using Mass Spectrometry
      Ugljesa Djuric, K. H. Brian Lam, Jennifer Kao, Ihor Batruch, Stefan Jevtic, Michail-Dimitrios Papaioannou and Phedias Diamandis
      Molecular & Cellular Proteomics October 1, 2019, First published on July 28, 2019, 18 (10) 2029-2043; https://doi.org/10.1074/mcp.RA119.001521

      Gliomas represent the most common brain tumor type. Molecular and global omics are becoming powerful tools for tumor subclassification that will facilitate more subtype-specific treatment options for patients. Here, we demonstrate that proteomic-based subclassification of closely related gliomas, differentiated by IDH mutation and 1p19q chromosome codeletion status, is facilitated by tumor microdissections prior to mass spectrometry analysis. Identified protein modules are confirmed in tissue culture grown glioma stem cells and point to chloride transport and stress proteins as strong drivers of glioma molecular diversions.

  2. Papanastasiou, Malvina

    1. Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS
      You have access
      Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS
      Malvina Papanastasiou, James Mullahoo, Katherine C. DeRuff, Besnik Bajrami, Ioannis Karageorgos, Stephen E. Johnston, Ryan Peckner, Samuel A. Myers, Steven A. Carr and Jacob D. Jaffe
      Molecular & Cellular Proteomics October 1, 2019, First published on August 13, 2019, 18 (10) 2089-2098; https://doi.org/10.1074/mcp.RA119.001325

      Cathepsin-L, a protease known to proteolyse histone tails in cells, is introduced as a novel enzyme for HX-MS. Cathepsin-L generates overlapping N-terminal peptides, improving coverage of histone tails that are poorly represented in HX-MS employing pepsin alone. Cathepsin-L/pepsin is employed to investigate in-solution dynamics of H3 and H4 monomers. Rapid deuteration of the tails is indicative of unfolded polypeptides, whereas extensive bimodal distributions detected in the histone-folds reveal cooperative unfolding events.

  3. Paz-González, Rocío

    1. Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      You have access
      Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      Patricia Fernández-Puente, Lucía González-Rodríguez, Valentina Calamia, Florencia Picchi, Lucía Lourido, María Camacho-Encina, Natividad Oreiro, Beatriz Rocha, Rocío Paz-González, Anabel Marina, Carlos García, Francisco J. Blanco and Cristina Ruiz-Romero
      Molecular & Cellular Proteomics October 1, 2019, First published on July 27, 2019, 18 (10) 2018-2028; https://doi.org/10.1074/mcp.RA119.001554

      Osteoarthritis (OA) is a disease primarily characterized by the loss of cartilage extracellular matrix. We have followed a peptidomic strategy to identify endogenous peptides (neopeptides) released from healthy and OA human knee and hip articular cartilage, which may serve as disease markers. This study provides a comprehensive neopeptidomic profile of healthy and diseased tissues, and the identification and validation of a panel of eight endogenous peptides that are differentially released from the extracellular matrix because of the pathogenic process.

  4. Peckner, Ryan

    1. Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS
      You have access
      Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS
      Malvina Papanastasiou, James Mullahoo, Katherine C. DeRuff, Besnik Bajrami, Ioannis Karageorgos, Stephen E. Johnston, Ryan Peckner, Samuel A. Myers, Steven A. Carr and Jacob D. Jaffe
      Molecular & Cellular Proteomics October 1, 2019, First published on August 13, 2019, 18 (10) 2089-2098; https://doi.org/10.1074/mcp.RA119.001325

      Cathepsin-L, a protease known to proteolyse histone tails in cells, is introduced as a novel enzyme for HX-MS. Cathepsin-L generates overlapping N-terminal peptides, improving coverage of histone tails that are poorly represented in HX-MS employing pepsin alone. Cathepsin-L/pepsin is employed to investigate in-solution dynamics of H3 and H4 monomers. Rapid deuteration of the tails is indicative of unfolded polypeptides, whereas extensive bimodal distributions detected in the histone-folds reveal cooperative unfolding events.

  5. Peng, Yanfei

    1. Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Open Access
      Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Nian Wu, Lisete M. Silva, Yan Liu, Yibing Zhang, Chao Gao, Fuming Zhang, Li Fu, Yanfei Peng, Robert Linhardt, Toshisuke Kawasaki, Barbara Mulloy, Wengang Chai and Ten Feizi
      Molecular & Cellular Proteomics October 1, 2019, First published on July 15, 2019, 18 (10) 1981-2002; https://doi.org/10.1074/mcp.RA119.001309

      R-10G antigen of human iPS and ES cells has been assigned as a unique mono-sulfated glycan. We highlight its relationship to a known bioactive glycan sequence, the ligand on high endothelial venules for the lymphocyte homing receptor, L-selectin. Details of the sequences of four other glycan antigens on the podocalyxin are re-evaluated and ambiguities resolved. Regulation of biosynthesis and possible involvements of these glycans in podocalyxin-signaling in stem cells are discussed.

  6. Peshkin, Leonid

    1. Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-statistics with Peptide Quantification Concordance
      You have access
      Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-statistics with Peptide Quantification Concordance
      Leonid Peshkin, Meera Gupta, Lillia Ryazanova and Martin Wühr
      Molecular & Cellular Proteomics October 1, 2019, First published on July 16, 2019, 18 (10) 2108-2120; https://doi.org/10.1074/mcp.TIR119.001317

      Multiplexed proteomics has become a powerful tool to assay biological systems. So far, the data is typically interpreted via naive peptide averaging. Here, we present a Bayesian approach that integrates peptide quantification concordance and ion statistics into the most probable answer with confidence intervals. Our approach considers low signal peptides, does not require replicates, and detects smaller significant changes than alternative approaches. Thus, our method increases the value of proteomics experiments, helping researchers to interpret data and prioritize resources.

  7. Peters, Kevin

    1. Vascular Endothelial Receptor Tyrosine Phosphatase: Identification of Novel Substrates Related to Junctions and a Ternary Complex with EPHB4 and TIE2
      You have access
      Vascular Endothelial Receptor Tyrosine Phosphatase: Identification of Novel Substrates Related to Junctions and a Ternary Complex with EPHB4 and TIE2
      Hannes C. A. Drexler, Matthias Vockel, Christian Polaschegg, Maike Frye, Kevin Peters and Dietmar Vestweber
      Molecular & Cellular Proteomics October 1, 2019, First published on August 19, 2019, 18 (10) 2058-2077; https://doi.org/10.1074/mcp.RA119.001716

      The phosphoproteome of the endothelial receptor type tyrosine phosphatase VE-PTP has been identified for mouse endothelial cells by a substrate trapping approach and a second anti-phosphotyrosine affinity isolation approach. In agreement with the central role of VE-PTP as regulator of endothelial junctions, 29% of the identified substrate candidates were junction related. Besides the well characterized substrates Tie-2 and FGD5, the tyrosine kinase receptor EPHB4 was identified as novel substrate, which formed a ternary complex with VE-PTP and Tie-2.

  8. Pham, Linda

    1. Delta-S-Cys-Albumin: A Lab Test that Quantifies Cumulative Exposure of Archived Human Blood Plasma and Serum Samples to Thawed Conditions
      Open Access
      Delta-S-Cys-Albumin: A Lab Test that Quantifies Cumulative Exposure of Archived Human Blood Plasma and Serum Samples to Thawed Conditions
      Joshua W. Jeffs, Nilojan Jehanathan, Stephanie M. F. Thibert, Shadi Ferdosi, Linda Pham, Zachary T. Wilson, Christian Breburda and Chad R. Borges
      Molecular & Cellular Proteomics October 1, 2019, First published on July 19, 2019, 18 (10) 2121-2137; https://doi.org/10.1074/mcp.TIR119.001659

      ΔS-Cys-Albumin, an endogenous marker of plasma and serum (P/S) exposure to thawed conditions (> −30 °C) based on the ex vivo S-cysteinylation (oxidizability) of albumin was developed. Average values in fresh P/S samples from a population of nonacute cardiac patients were determined. The multireaction mechanism that drives changes in albumin S-cysteinylation is known and the rate law for it has been established and accurately modeled in P/S. Measurement of ΔS-Cys-Albumin in unknown samples facilitates estimation of thawed-state exposure times.

  9. Picchi, Florencia

    1. Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      You have access
      Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      Patricia Fernández-Puente, Lucía González-Rodríguez, Valentina Calamia, Florencia Picchi, Lucía Lourido, María Camacho-Encina, Natividad Oreiro, Beatriz Rocha, Rocío Paz-González, Anabel Marina, Carlos García, Francisco J. Blanco and Cristina Ruiz-Romero
      Molecular & Cellular Proteomics October 1, 2019, First published on July 27, 2019, 18 (10) 2018-2028; https://doi.org/10.1074/mcp.RA119.001554

      Osteoarthritis (OA) is a disease primarily characterized by the loss of cartilage extracellular matrix. We have followed a peptidomic strategy to identify endogenous peptides (neopeptides) released from healthy and OA human knee and hip articular cartilage, which may serve as disease markers. This study provides a comprehensive neopeptidomic profile of healthy and diseased tissues, and the identification and validation of a panel of eight endogenous peptides that are differentially released from the extracellular matrix because of the pathogenic process.

  10. Polaschegg, Christian

    1. Vascular Endothelial Receptor Tyrosine Phosphatase: Identification of Novel Substrates Related to Junctions and a Ternary Complex with EPHB4 and TIE2
      You have access
      Vascular Endothelial Receptor Tyrosine Phosphatase: Identification of Novel Substrates Related to Junctions and a Ternary Complex with EPHB4 and TIE2
      Hannes C. A. Drexler, Matthias Vockel, Christian Polaschegg, Maike Frye, Kevin Peters and Dietmar Vestweber
      Molecular & Cellular Proteomics October 1, 2019, First published on August 19, 2019, 18 (10) 2058-2077; https://doi.org/10.1074/mcp.RA119.001716

      The phosphoproteome of the endothelial receptor type tyrosine phosphatase VE-PTP has been identified for mouse endothelial cells by a substrate trapping approach and a second anti-phosphotyrosine affinity isolation approach. In agreement with the central role of VE-PTP as regulator of endothelial junctions, 29% of the identified substrate candidates were junction related. Besides the well characterized substrates Tie-2 and FGD5, the tyrosine kinase receptor EPHB4 was identified as novel substrate, which formed a ternary complex with VE-PTP and Tie-2.

R

  1. Rafii, Arash

    1. A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      You have access
      A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      Anja M. Billing, Shaima S. Dib, Aditya M. Bhagwat, Israel T. da Silva, Rodrigo D. Drummond, Shahina Hayat, Rasha Al-Mismar, Hisham Ben-Hamidane, Neha Goswami, Kasper Engholm-Keller, Martin R. Larsen, Karsten Suhre, Arash Rafii and Johannes Graumann
      Molecular & Cellular Proteomics October 1, 2019, First published on July 22, 2019, 18 (10) 1950-1966; https://doi.org/10.1074/mcp.RA119.001356

      In this integrative, multi-omics study we characterized the differentiation of human embryonic stem cells into mesenchymal stem cells using transcriptomics, quantitative MS-based proteomics and phosphoproteomics. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation with AHNAK hypothesized to be a defining factor in MSC biology. Additional central findings include two distinct expression waves of developmental HOX genes as well as an AGO2-to-AGO3 switch in gene silencing.

  2. Ren, Shuangxi

    1. <em>Sc</em>CobB2-mediated Lysine Desuccinylation Regulates Protein Biosynthesis and Carbon Metabolism in <em>Streptomyces coelicolor</em>
      You have access
      ScCobB2-mediated Lysine Desuccinylation Regulates Protein Biosynthesis and Carbon Metabolism in Streptomyces coelicolor
      Hong Zhang, Peng Li, Shuangxi Ren, Zhongyi Cheng, Guoping Zhao and Wei Zhao
      Molecular & Cellular Proteomics October 1, 2019, First published on July 23, 2019, 18 (10) 2003-2017; https://doi.org/10.1074/mcp.RA118.001298

      Lysine succinylation is a prevalent protein modification that regulates multiple critical cellular processes. Here, we performed a quantitative succinylome analysis in the model soil bacterium Streptomyces coelicolor after characterization of a specific desuccinylase ScCobB2. Comparison of the ΔScCobB2 to the wild-type succinylome identified a total of 673 unique succinylated sites, and among which, 144 protein sites are statistically hypersuccinylated in ΔScCobB2 cells. Analyses of these hypersuccinylated proteins suggested they are enriched in two major pathways, protein biosynthesis and carbon metabolism. We propose that ScCobB2 has critical regulatory roles in S. coelicolor cellular physiology.

  3. Rocha, Beatriz

    1. Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      You have access
      Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      Patricia Fernández-Puente, Lucía González-Rodríguez, Valentina Calamia, Florencia Picchi, Lucía Lourido, María Camacho-Encina, Natividad Oreiro, Beatriz Rocha, Rocío Paz-González, Anabel Marina, Carlos García, Francisco J. Blanco and Cristina Ruiz-Romero
      Molecular & Cellular Proteomics October 1, 2019, First published on July 27, 2019, 18 (10) 2018-2028; https://doi.org/10.1074/mcp.RA119.001554

      Osteoarthritis (OA) is a disease primarily characterized by the loss of cartilage extracellular matrix. We have followed a peptidomic strategy to identify endogenous peptides (neopeptides) released from healthy and OA human knee and hip articular cartilage, which may serve as disease markers. This study provides a comprehensive neopeptidomic profile of healthy and diseased tissues, and the identification and validation of a panel of eight endogenous peptides that are differentially released from the extracellular matrix because of the pathogenic process.

  4. Ruiz-Romero, Cristina

    1. Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      You have access
      Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers
      Patricia Fernández-Puente, Lucía González-Rodríguez, Valentina Calamia, Florencia Picchi, Lucía Lourido, María Camacho-Encina, Natividad Oreiro, Beatriz Rocha, Rocío Paz-González, Anabel Marina, Carlos García, Francisco J. Blanco and Cristina Ruiz-Romero
      Molecular & Cellular Proteomics October 1, 2019, First published on July 27, 2019, 18 (10) 2018-2028; https://doi.org/10.1074/mcp.RA119.001554

      Osteoarthritis (OA) is a disease primarily characterized by the loss of cartilage extracellular matrix. We have followed a peptidomic strategy to identify endogenous peptides (neopeptides) released from healthy and OA human knee and hip articular cartilage, which may serve as disease markers. This study provides a comprehensive neopeptidomic profile of healthy and diseased tissues, and the identification and validation of a panel of eight endogenous peptides that are differentially released from the extracellular matrix because of the pathogenic process.

  5. Ryazanova, Lillia

    1. Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-statistics with Peptide Quantification Concordance
      You have access
      Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-statistics with Peptide Quantification Concordance
      Leonid Peshkin, Meera Gupta, Lillia Ryazanova and Martin Wühr
      Molecular & Cellular Proteomics October 1, 2019, First published on July 16, 2019, 18 (10) 2108-2120; https://doi.org/10.1074/mcp.TIR119.001317

      Multiplexed proteomics has become a powerful tool to assay biological systems. So far, the data is typically interpreted via naive peptide averaging. Here, we present a Bayesian approach that integrates peptide quantification concordance and ion statistics into the most probable answer with confidence intervals. Our approach considers low signal peptides, does not require replicates, and detects smaller significant changes than alternative approaches. Thus, our method increases the value of proteomics experiments, helping researchers to interpret data and prioritize resources.

S

  1. Sato, Keiko

    1. Bisecting GlcNAc Is a General Suppressor of Terminal Modification of <em>N</em>-glycan
      You have access
      Bisecting GlcNAc Is a General Suppressor of Terminal Modification of N-glycan
      Miyako Nakano, Sushil K. Mishra, Yuko Tokoro, Keiko Sato, Kazuki Nakajima, Yoshiki Yamaguchi, Naoyuki Taniguchi and Yasuhiko Kizuka
      Molecular & Cellular Proteomics October 1, 2019, First published on August 2, 2019, 18 (10) 2044-2057; https://doi.org/10.1074/mcp.RA119.001534

      Bisecting GlcNAc, a branching sugar in N-glycan highly expressed in brain, is involved in Alzheimer's disease, but its physiological function is largely unclear. In this manuscript, the authors revealed that loss of bisecting GlcNAc in mice leads to upregulation of various types of terminal modifications of N-glycans. As a mechanism, many glycosyltransferases were found to commonly prefer glycans without bisecting GlcNAc as a substrate. These data indicate that bisecting GlcNAc generally suppresses terminal modifications of N-glycans.

  2. Silva, Lisete M.

    1. Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Open Access
      Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Nian Wu, Lisete M. Silva, Yan Liu, Yibing Zhang, Chao Gao, Fuming Zhang, Li Fu, Yanfei Peng, Robert Linhardt, Toshisuke Kawasaki, Barbara Mulloy, Wengang Chai and Ten Feizi
      Molecular & Cellular Proteomics October 1, 2019, First published on July 15, 2019, 18 (10) 1981-2002; https://doi.org/10.1074/mcp.RA119.001309

      R-10G antigen of human iPS and ES cells has been assigned as a unique mono-sulfated glycan. We highlight its relationship to a known bioactive glycan sequence, the ligand on high endothelial venules for the lymphocyte homing receptor, L-selectin. Details of the sequences of four other glycan antigens on the podocalyxin are re-evaluated and ambiguities resolved. Regulation of biosynthesis and possible involvements of these glycans in podocalyxin-signaling in stem cells are discussed.

  3. Suhre, Karsten

    1. A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      You have access
      A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
      Anja M. Billing, Shaima S. Dib, Aditya M. Bhagwat, Israel T. da Silva, Rodrigo D. Drummond, Shahina Hayat, Rasha Al-Mismar, Hisham Ben-Hamidane, Neha Goswami, Kasper Engholm-Keller, Martin R. Larsen, Karsten Suhre, Arash Rafii and Johannes Graumann
      Molecular & Cellular Proteomics October 1, 2019, First published on July 22, 2019, 18 (10) 1950-1966; https://doi.org/10.1074/mcp.RA119.001356

      In this integrative, multi-omics study we characterized the differentiation of human embryonic stem cells into mesenchymal stem cells using transcriptomics, quantitative MS-based proteomics and phosphoproteomics. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation with AHNAK hypothesized to be a defining factor in MSC biology. Additional central findings include two distinct expression waves of developmental HOX genes as well as an AGO2-to-AGO3 switch in gene silencing.

T

  1. Taniguchi, Naoyuki

    1. Bisecting GlcNAc Is a General Suppressor of Terminal Modification of <em>N</em>-glycan
      You have access
      Bisecting GlcNAc Is a General Suppressor of Terminal Modification of N-glycan
      Miyako Nakano, Sushil K. Mishra, Yuko Tokoro, Keiko Sato, Kazuki Nakajima, Yoshiki Yamaguchi, Naoyuki Taniguchi and Yasuhiko Kizuka
      Molecular & Cellular Proteomics October 1, 2019, First published on August 2, 2019, 18 (10) 2044-2057; https://doi.org/10.1074/mcp.RA119.001534

      Bisecting GlcNAc, a branching sugar in N-glycan highly expressed in brain, is involved in Alzheimer's disease, but its physiological function is largely unclear. In this manuscript, the authors revealed that loss of bisecting GlcNAc in mice leads to upregulation of various types of terminal modifications of N-glycans. As a mechanism, many glycosyltransferases were found to commonly prefer glycans without bisecting GlcNAc as a substrate. These data indicate that bisecting GlcNAc generally suppresses terminal modifications of N-glycans.

  2. Thibert, Stephanie M. F.

    1. Delta-S-Cys-Albumin: A Lab Test that Quantifies Cumulative Exposure of Archived Human Blood Plasma and Serum Samples to Thawed Conditions
      Open Access
      Delta-S-Cys-Albumin: A Lab Test that Quantifies Cumulative Exposure of Archived Human Blood Plasma and Serum Samples to Thawed Conditions
      Joshua W. Jeffs, Nilojan Jehanathan, Stephanie M. F. Thibert, Shadi Ferdosi, Linda Pham, Zachary T. Wilson, Christian Breburda and Chad R. Borges
      Molecular & Cellular Proteomics October 1, 2019, First published on July 19, 2019, 18 (10) 2121-2137; https://doi.org/10.1074/mcp.TIR119.001659

      ΔS-Cys-Albumin, an endogenous marker of plasma and serum (P/S) exposure to thawed conditions (> −30 °C) based on the ex vivo S-cysteinylation (oxidizability) of albumin was developed. Average values in fresh P/S samples from a population of nonacute cardiac patients were determined. The multireaction mechanism that drives changes in albumin S-cysteinylation is known and the rate law for it has been established and accurately modeled in P/S. Measurement of ΔS-Cys-Albumin in unknown samples facilitates estimation of thawed-state exposure times.

  3. Tokoro, Yuko

    1. Bisecting GlcNAc Is a General Suppressor of Terminal Modification of <em>N</em>-glycan
      You have access
      Bisecting GlcNAc Is a General Suppressor of Terminal Modification of N-glycan
      Miyako Nakano, Sushil K. Mishra, Yuko Tokoro, Keiko Sato, Kazuki Nakajima, Yoshiki Yamaguchi, Naoyuki Taniguchi and Yasuhiko Kizuka
      Molecular & Cellular Proteomics October 1, 2019, First published on August 2, 2019, 18 (10) 2044-2057; https://doi.org/10.1074/mcp.RA119.001534

      Bisecting GlcNAc, a branching sugar in N-glycan highly expressed in brain, is involved in Alzheimer's disease, but its physiological function is largely unclear. In this manuscript, the authors revealed that loss of bisecting GlcNAc in mice leads to upregulation of various types of terminal modifications of N-glycans. As a mechanism, many glycosyltransferases were found to commonly prefer glycans without bisecting GlcNAc as a substrate. These data indicate that bisecting GlcNAc generally suppresses terminal modifications of N-glycans.

V

  1. Vestweber, Dietmar

    1. Vascular Endothelial Receptor Tyrosine Phosphatase: Identification of Novel Substrates Related to Junctions and a Ternary Complex with EPHB4 and TIE2
      You have access
      Vascular Endothelial Receptor Tyrosine Phosphatase: Identification of Novel Substrates Related to Junctions and a Ternary Complex with EPHB4 and TIE2
      Hannes C. A. Drexler, Matthias Vockel, Christian Polaschegg, Maike Frye, Kevin Peters and Dietmar Vestweber
      Molecular & Cellular Proteomics October 1, 2019, First published on August 19, 2019, 18 (10) 2058-2077; https://doi.org/10.1074/mcp.RA119.001716

      The phosphoproteome of the endothelial receptor type tyrosine phosphatase VE-PTP has been identified for mouse endothelial cells by a substrate trapping approach and a second anti-phosphotyrosine affinity isolation approach. In agreement with the central role of VE-PTP as regulator of endothelial junctions, 29% of the identified substrate candidates were junction related. Besides the well characterized substrates Tie-2 and FGD5, the tyrosine kinase receptor EPHB4 was identified as novel substrate, which formed a ternary complex with VE-PTP and Tie-2.

  2. Vockel, Matthias

    1. Vascular Endothelial Receptor Tyrosine Phosphatase: Identification of Novel Substrates Related to Junctions and a Ternary Complex with EPHB4 and TIE2
      You have access
      Vascular Endothelial Receptor Tyrosine Phosphatase: Identification of Novel Substrates Related to Junctions and a Ternary Complex with EPHB4 and TIE2
      Hannes C. A. Drexler, Matthias Vockel, Christian Polaschegg, Maike Frye, Kevin Peters and Dietmar Vestweber
      Molecular & Cellular Proteomics October 1, 2019, First published on August 19, 2019, 18 (10) 2058-2077; https://doi.org/10.1074/mcp.RA119.001716

      The phosphoproteome of the endothelial receptor type tyrosine phosphatase VE-PTP has been identified for mouse endothelial cells by a substrate trapping approach and a second anti-phosphotyrosine affinity isolation approach. In agreement with the central role of VE-PTP as regulator of endothelial junctions, 29% of the identified substrate candidates were junction related. Besides the well characterized substrates Tie-2 and FGD5, the tyrosine kinase receptor EPHB4 was identified as novel substrate, which formed a ternary complex with VE-PTP and Tie-2.

W

  1. Wilson, Zachary T.

    1. Delta-S-Cys-Albumin: A Lab Test that Quantifies Cumulative Exposure of Archived Human Blood Plasma and Serum Samples to Thawed Conditions
      Open Access
      Delta-S-Cys-Albumin: A Lab Test that Quantifies Cumulative Exposure of Archived Human Blood Plasma and Serum Samples to Thawed Conditions
      Joshua W. Jeffs, Nilojan Jehanathan, Stephanie M. F. Thibert, Shadi Ferdosi, Linda Pham, Zachary T. Wilson, Christian Breburda and Chad R. Borges
      Molecular & Cellular Proteomics October 1, 2019, First published on July 19, 2019, 18 (10) 2121-2137; https://doi.org/10.1074/mcp.TIR119.001659

      ΔS-Cys-Albumin, an endogenous marker of plasma and serum (P/S) exposure to thawed conditions (> −30 °C) based on the ex vivo S-cysteinylation (oxidizability) of albumin was developed. Average values in fresh P/S samples from a population of nonacute cardiac patients were determined. The multireaction mechanism that drives changes in albumin S-cysteinylation is known and the rate law for it has been established and accurately modeled in P/S. Measurement of ΔS-Cys-Albumin in unknown samples facilitates estimation of thawed-state exposure times.

  2. Wlodarczyk, Jakub

    1. Stress-induced Changes in the S-palmitoylation and S-nitrosylation of Synaptic Proteins
      You have access
      Stress-induced Changes in the S-palmitoylation and S-nitrosylation of Synaptic Proteins
      Monika Zareba-Koziol, Anna Bartkowiak-Kaczmarek, Izabela Figiel, Adam Krzystyniak, Tomasz Wojtowicz, Monika Bijata and Jakub Wlodarczyk
      Molecular & Cellular Proteomics October 1, 2019, First published on July 16, 2019, 18 (10) 1916-1938; https://doi.org/10.1074/mcp.RA119.001581

      To improve simultaneous S-palmitoylation and S-nitrosylation site profiling, we developed a novel mass spectrometry-based strategy Palmitoylation And Nitrosylation Interplay Monitoring (PANIMoni). Using this approach we evaluated dynamic, site-specific changes in two important cysteine modifications, S-PALM and S-NO, in a mouse model of chronic stress. High-throughput analysis provided valuable insight into chronic, stress-induced remodeling of the synaptic proteome. Based on the obtained data, we postulate that the mechanism underlying chronic stress involves mutual competition between S-PALM and S-NO for modification sites.

  3. Wojtowicz, Tomasz

    1. Stress-induced Changes in the S-palmitoylation and S-nitrosylation of Synaptic Proteins
      You have access
      Stress-induced Changes in the S-palmitoylation and S-nitrosylation of Synaptic Proteins
      Monika Zareba-Koziol, Anna Bartkowiak-Kaczmarek, Izabela Figiel, Adam Krzystyniak, Tomasz Wojtowicz, Monika Bijata and Jakub Wlodarczyk
      Molecular & Cellular Proteomics October 1, 2019, First published on July 16, 2019, 18 (10) 1916-1938; https://doi.org/10.1074/mcp.RA119.001581

      To improve simultaneous S-palmitoylation and S-nitrosylation site profiling, we developed a novel mass spectrometry-based strategy Palmitoylation And Nitrosylation Interplay Monitoring (PANIMoni). Using this approach we evaluated dynamic, site-specific changes in two important cysteine modifications, S-PALM and S-NO, in a mouse model of chronic stress. High-throughput analysis provided valuable insight into chronic, stress-induced remodeling of the synaptic proteome. Based on the obtained data, we postulate that the mechanism underlying chronic stress involves mutual competition between S-PALM and S-NO for modification sites.

  4. Wu, Chih-Ching

    1. Proteomic Profiling of Paired Interstitial Fluids Reveals Dysregulated Pathways and Salivary NID1 as a Biomarker of Oral Cavity Squamous Cell Carcinoma
      You have access
      Proteomic Profiling of Paired Interstitial Fluids Reveals Dysregulated Pathways and Salivary NID1 as a Biomarker of Oral Cavity Squamous Cell Carcinoma
      Chia-Wei Hsu, Kai-Ping Chang, Yenlin Huang, Hao-Ping Liu, Pei-Chun Hsueh, Po-Wen Gu, Wei-Chen Yen and Chih-Ching Wu
      Molecular & Cellular Proteomics October 1, 2019, First published on July 17, 2019, 18 (10) 1939-1949; https://doi.org/10.1074/mcp.RA119.001654

      Oral cavity squamous cell carcinoma (OSCC) is frequently diagnosed at an advanced stage, leading to poor prognosis and high mortality rate. To develop method for OSCC detection, proteome of tumor interstitial fluids (TIFs) has been profiled. The proteins differentially expressed in TIFs were highly associated with aminoacyl tRNA biosynthesis pathway. Importantly, nidogen-1 is a potential diagnostic and/or prognostic biomarker. The results suggest that TIF analysis facilitates understanding of OSCC microenvironment and discovery of biomarker candidates.

  5. Wu, Nian

    1. Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Open Access
      Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Nian Wu, Lisete M. Silva, Yan Liu, Yibing Zhang, Chao Gao, Fuming Zhang, Li Fu, Yanfei Peng, Robert Linhardt, Toshisuke Kawasaki, Barbara Mulloy, Wengang Chai and Ten Feizi
      Molecular & Cellular Proteomics October 1, 2019, First published on July 15, 2019, 18 (10) 1981-2002; https://doi.org/10.1074/mcp.RA119.001309

      R-10G antigen of human iPS and ES cells has been assigned as a unique mono-sulfated glycan. We highlight its relationship to a known bioactive glycan sequence, the ligand on high endothelial venules for the lymphocyte homing receptor, L-selectin. Details of the sequences of four other glycan antigens on the podocalyxin are re-evaluated and ambiguities resolved. Regulation of biosynthesis and possible involvements of these glycans in podocalyxin-signaling in stem cells are discussed.

  6. Wühr, Martin

    1. Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-statistics with Peptide Quantification Concordance
      You have access
      Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-statistics with Peptide Quantification Concordance
      Leonid Peshkin, Meera Gupta, Lillia Ryazanova and Martin Wühr
      Molecular & Cellular Proteomics October 1, 2019, First published on July 16, 2019, 18 (10) 2108-2120; https://doi.org/10.1074/mcp.TIR119.001317

      Multiplexed proteomics has become a powerful tool to assay biological systems. So far, the data is typically interpreted via naive peptide averaging. Here, we present a Bayesian approach that integrates peptide quantification concordance and ion statistics into the most probable answer with confidence intervals. Our approach considers low signal peptides, does not require replicates, and detects smaller significant changes than alternative approaches. Thus, our method increases the value of proteomics experiments, helping researchers to interpret data and prioritize resources.

Y

  1. Yamaguchi, Yoshiki

    1. Bisecting GlcNAc Is a General Suppressor of Terminal Modification of <em>N</em>-glycan
      You have access
      Bisecting GlcNAc Is a General Suppressor of Terminal Modification of N-glycan
      Miyako Nakano, Sushil K. Mishra, Yuko Tokoro, Keiko Sato, Kazuki Nakajima, Yoshiki Yamaguchi, Naoyuki Taniguchi and Yasuhiko Kizuka
      Molecular & Cellular Proteomics October 1, 2019, First published on August 2, 2019, 18 (10) 2044-2057; https://doi.org/10.1074/mcp.RA119.001534

      Bisecting GlcNAc, a branching sugar in N-glycan highly expressed in brain, is involved in Alzheimer's disease, but its physiological function is largely unclear. In this manuscript, the authors revealed that loss of bisecting GlcNAc in mice leads to upregulation of various types of terminal modifications of N-glycans. As a mechanism, many glycosyltransferases were found to commonly prefer glycans without bisecting GlcNAc as a substrate. These data indicate that bisecting GlcNAc generally suppresses terminal modifications of N-glycans.

  2. Yang, Lu

    1. Multidimensional Proteomics Identifies Declines in Protein Homeostasis and Mitochondria as Early Signals for Normal Aging and Age-associated Disease in <em>Drosophila</em>
      You have access
      Multidimensional Proteomics Identifies Declines in Protein Homeostasis and Mitochondria as Early Signals for Normal Aging and Age-associated Disease in Drosophila
      Lu Yang, Ye Cao, Jing Zhao, Yanshan Fang, Nan Liu and Yaoyang Zhang
      Molecular & Cellular Proteomics October 1, 2019, First published on August 21, 2019, 18 (10) 2078-2088; https://doi.org/10.1074/mcp.RA119.001621

      Yang et al. have profiled the snapshot and dynamics of the proteomes from Drosophila somatic and reproductive tissues during aging, revealing both tissue-specific and common pathways that are modulated with age. Analysis of proteome dynamics demonstrates that the global protein synthesis, particularly for those proteins functionally related to proteostasis and mitochondria, is down-regulated during normal aging, and that this decline becomes dramatically enhanced in the Drosophila model of human Parkinson's disease.

  3. Yen, Wei-Chen

    1. Proteomic Profiling of Paired Interstitial Fluids Reveals Dysregulated Pathways and Salivary NID1 as a Biomarker of Oral Cavity Squamous Cell Carcinoma
      You have access
      Proteomic Profiling of Paired Interstitial Fluids Reveals Dysregulated Pathways and Salivary NID1 as a Biomarker of Oral Cavity Squamous Cell Carcinoma
      Chia-Wei Hsu, Kai-Ping Chang, Yenlin Huang, Hao-Ping Liu, Pei-Chun Hsueh, Po-Wen Gu, Wei-Chen Yen and Chih-Ching Wu
      Molecular & Cellular Proteomics October 1, 2019, First published on July 17, 2019, 18 (10) 1939-1949; https://doi.org/10.1074/mcp.RA119.001654

      Oral cavity squamous cell carcinoma (OSCC) is frequently diagnosed at an advanced stage, leading to poor prognosis and high mortality rate. To develop method for OSCC detection, proteome of tumor interstitial fluids (TIFs) has been profiled. The proteins differentially expressed in TIFs were highly associated with aminoacyl tRNA biosynthesis pathway. Importantly, nidogen-1 is a potential diagnostic and/or prognostic biomarker. The results suggest that TIF analysis facilitates understanding of OSCC microenvironment and discovery of biomarker candidates.

Z

  1. Zareba-Koziol, Monika

    1. Stress-induced Changes in the S-palmitoylation and S-nitrosylation of Synaptic Proteins
      You have access
      Stress-induced Changes in the S-palmitoylation and S-nitrosylation of Synaptic Proteins
      Monika Zareba-Koziol, Anna Bartkowiak-Kaczmarek, Izabela Figiel, Adam Krzystyniak, Tomasz Wojtowicz, Monika Bijata and Jakub Wlodarczyk
      Molecular & Cellular Proteomics October 1, 2019, First published on July 16, 2019, 18 (10) 1916-1938; https://doi.org/10.1074/mcp.RA119.001581

      To improve simultaneous S-palmitoylation and S-nitrosylation site profiling, we developed a novel mass spectrometry-based strategy Palmitoylation And Nitrosylation Interplay Monitoring (PANIMoni). Using this approach we evaluated dynamic, site-specific changes in two important cysteine modifications, S-PALM and S-NO, in a mouse model of chronic stress. High-throughput analysis provided valuable insight into chronic, stress-induced remodeling of the synaptic proteome. Based on the obtained data, we postulate that the mechanism underlying chronic stress involves mutual competition between S-PALM and S-NO for modification sites.

  2. Zhang, Fuming

    1. Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Open Access
      Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Nian Wu, Lisete M. Silva, Yan Liu, Yibing Zhang, Chao Gao, Fuming Zhang, Li Fu, Yanfei Peng, Robert Linhardt, Toshisuke Kawasaki, Barbara Mulloy, Wengang Chai and Ten Feizi
      Molecular & Cellular Proteomics October 1, 2019, First published on July 15, 2019, 18 (10) 1981-2002; https://doi.org/10.1074/mcp.RA119.001309

      R-10G antigen of human iPS and ES cells has been assigned as a unique mono-sulfated glycan. We highlight its relationship to a known bioactive glycan sequence, the ligand on high endothelial venules for the lymphocyte homing receptor, L-selectin. Details of the sequences of four other glycan antigens on the podocalyxin are re-evaluated and ambiguities resolved. Regulation of biosynthesis and possible involvements of these glycans in podocalyxin-signaling in stem cells are discussed.

  3. Zhang, Hong

    1. <em>Sc</em>CobB2-mediated Lysine Desuccinylation Regulates Protein Biosynthesis and Carbon Metabolism in <em>Streptomyces coelicolor</em>
      You have access
      ScCobB2-mediated Lysine Desuccinylation Regulates Protein Biosynthesis and Carbon Metabolism in Streptomyces coelicolor
      Hong Zhang, Peng Li, Shuangxi Ren, Zhongyi Cheng, Guoping Zhao and Wei Zhao
      Molecular & Cellular Proteomics October 1, 2019, First published on July 23, 2019, 18 (10) 2003-2017; https://doi.org/10.1074/mcp.RA118.001298

      Lysine succinylation is a prevalent protein modification that regulates multiple critical cellular processes. Here, we performed a quantitative succinylome analysis in the model soil bacterium Streptomyces coelicolor after characterization of a specific desuccinylase ScCobB2. Comparison of the ΔScCobB2 to the wild-type succinylome identified a total of 673 unique succinylated sites, and among which, 144 protein sites are statistically hypersuccinylated in ΔScCobB2 cells. Analyses of these hypersuccinylated proteins suggested they are enriched in two major pathways, protein biosynthesis and carbon metabolism. We propose that ScCobB2 has critical regulatory roles in S. coelicolor cellular physiology.

  4. Zhang, Yaoyang

    1. Multidimensional Proteomics Identifies Declines in Protein Homeostasis and Mitochondria as Early Signals for Normal Aging and Age-associated Disease in <em>Drosophila</em>
      You have access
      Multidimensional Proteomics Identifies Declines in Protein Homeostasis and Mitochondria as Early Signals for Normal Aging and Age-associated Disease in Drosophila
      Lu Yang, Ye Cao, Jing Zhao, Yanshan Fang, Nan Liu and Yaoyang Zhang
      Molecular & Cellular Proteomics October 1, 2019, First published on August 21, 2019, 18 (10) 2078-2088; https://doi.org/10.1074/mcp.RA119.001621

      Yang et al. have profiled the snapshot and dynamics of the proteomes from Drosophila somatic and reproductive tissues during aging, revealing both tissue-specific and common pathways that are modulated with age. Analysis of proteome dynamics demonstrates that the global protein synthesis, particularly for those proteins functionally related to proteostasis and mitochondria, is down-regulated during normal aging, and that this decline becomes dramatically enhanced in the Drosophila model of human Parkinson's disease.

  5. Zhang, Yibing

    1. Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Open Access
      Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
      Nian Wu, Lisete M. Silva, Yan Liu, Yibing Zhang, Chao Gao, Fuming Zhang, Li Fu, Yanfei Peng, Robert Linhardt, Toshisuke Kawasaki, Barbara Mulloy, Wengang Chai and Ten Feizi
      Molecular & Cellular Proteomics October 1, 2019, First published on July 15, 2019, 18 (10) 1981-2002; https://doi.org/10.1074/mcp.RA119.001309

      R-10G antigen of human iPS and ES cells has been assigned as a unique mono-sulfated glycan. We highlight its relationship to a known bioactive glycan sequence, the ligand on high endothelial venules for the lymphocyte homing receptor, L-selectin. Details of the sequences of four other glycan antigens on the podocalyxin are re-evaluated and ambiguities resolved. Regulation of biosynthesis and possible involvements of these glycans in podocalyxin-signaling in stem cells are discussed.

  6. Zhao, Guoping

    1. <em>Sc</em>CobB2-mediated Lysine Desuccinylation Regulates Protein Biosynthesis and Carbon Metabolism in <em>Streptomyces coelicolor</em>
      You have access
      ScCobB2-mediated Lysine Desuccinylation Regulates Protein Biosynthesis and Carbon Metabolism in Streptomyces coelicolor
      Hong Zhang, Peng Li, Shuangxi Ren, Zhongyi Cheng, Guoping Zhao and Wei Zhao
      Molecular & Cellular Proteomics October 1, 2019, First published on July 23, 2019, 18 (10) 2003-2017; https://doi.org/10.1074/mcp.RA118.001298

      Lysine succinylation is a prevalent protein modification that regulates multiple critical cellular processes. Here, we performed a quantitative succinylome analysis in the model soil bacterium Streptomyces coelicolor after characterization of a specific desuccinylase ScCobB2. Comparison of the ΔScCobB2 to the wild-type succinylome identified a total of 673 unique succinylated sites, and among which, 144 protein sites are statistically hypersuccinylated in ΔScCobB2 cells. Analyses of these hypersuccinylated proteins suggested they are enriched in two major pathways, protein biosynthesis and carbon metabolism. We propose that ScCobB2 has critical regulatory roles in S. coelicolor cellular physiology.

  7. Zhao, Jing

    1. Multidimensional Proteomics Identifies Declines in Protein Homeostasis and Mitochondria as Early Signals for Normal Aging and Age-associated Disease in <em>Drosophila</em>
      You have access
      Multidimensional Proteomics Identifies Declines in Protein Homeostasis and Mitochondria as Early Signals for Normal Aging and Age-associated Disease in Drosophila
      Lu Yang, Ye Cao, Jing Zhao, Yanshan Fang, Nan Liu and Yaoyang Zhang
      Molecular & Cellular Proteomics October 1, 2019, First published on August 21, 2019, 18 (10) 2078-2088; https://doi.org/10.1074/mcp.RA119.001621

      Yang et al. have profiled the snapshot and dynamics of the proteomes from Drosophila somatic and reproductive tissues during aging, revealing both tissue-specific and common pathways that are modulated with age. Analysis of proteome dynamics demonstrates that the global protein synthesis, particularly for those proteins functionally related to proteostasis and mitochondria, is down-regulated during normal aging, and that this decline becomes dramatically enhanced in the Drosophila model of human Parkinson's disease.

  8. Zhao, Wei

    1. <em>Sc</em>CobB2-mediated Lysine Desuccinylation Regulates Protein Biosynthesis and Carbon Metabolism in <em>Streptomyces coelicolor</em>
      You have access
      ScCobB2-mediated Lysine Desuccinylation Regulates Protein Biosynthesis and Carbon Metabolism in Streptomyces coelicolor
      Hong Zhang, Peng Li, Shuangxi Ren, Zhongyi Cheng, Guoping Zhao and Wei Zhao
      Molecular & Cellular Proteomics October 1, 2019, First published on July 23, 2019, 18 (10) 2003-2017; https://doi.org/10.1074/mcp.RA118.001298

      Lysine succinylation is a prevalent protein modification that regulates multiple critical cellular processes. Here, we performed a quantitative succinylome analysis in the model soil bacterium Streptomyces coelicolor after characterization of a specific desuccinylase ScCobB2. Comparison of the ΔScCobB2 to the wild-type succinylome identified a total of 673 unique succinylated sites, and among which, 144 protein sites are statistically hypersuccinylated in ΔScCobB2 cells. Analyses of these hypersuccinylated proteins suggested they are enriched in two major pathways, protein biosynthesis and carbon metabolism. We propose that ScCobB2 has critical regulatory roles in S. coelicolor cellular physiology.

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Molecular & Cellular Proteomics: 18 (10)
Molecular & Cellular Proteomics
Vol. 18, Issue 10
1 Oct 2019
  • Table of Contents
  • Table of Contents (PDF)
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  • About the Cover
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Issue highlights

  • A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells
  • Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays
  • Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS
  • Prediction of LC-MS/MS Properties of Peptides from Sequence by Deep Learning
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