Index by author

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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-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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.