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Molecular & Cellular Proteomics

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2021

Volume 20

Open Access

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Published in issue: 2021

100183

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Editorial

Working Toward Reducing Bias in Peer Review

Kerry-Anne Rye,
Nicholas O. Davidson,
Alma L. Burlingame,
F. Peter Guengerich

Published online: September 27, 2021

100152

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Review

Proteome Turnover in the Spotlight: Approaches, Applications, and Perspectives

Proteome Turnover in the Spotlight: Approaches, Applications, and Perspectives

Alison Barbara Ross,
Julian David Langer,
Marko Jovanovic

Published online: December 06, 2020

100016

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Accelerating the Field of Epigenetic Histone Modification Through Mass Spectrometry–Based Approaches

Accelerating the Field of Epigenetic Histone Modification Through Mass Spectrometry–Based Approaches

Congcong Lu,
Mariel Coradin,
Elizabeth G. Porter,
Benjamin A. Garcia

Published online: December 07, 2020

100006

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Chromatin Proteomics to Study Epigenetics — Challenges and Opportunities

Chromatin Proteomics to Study Epigenetics — Challenges and Opportunities

Guido van Mierlo,
Michiel Vermeulen

Published online: February 05, 2021

100056

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Neuroproteomics of the Synapse: Subcellular Quantification of Protein Networks and Signaling Dynamics

Neuroproteomics of the Synapse: Subcellular Quantification of Protein Networks and Signaling Dynamics

Charlotte A.G.H. van Gelder,
Maarten Altelaar

Published online: April 28, 2021

100087

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Proteomics-Based Insights Into the SARS-CoV-2–Mediated COVID-19 Pandemic: A Review of the First Year of Research

Proteomics-Based Insights Into the SARS-CoV-2–Mediated COVID-19 Pandemic: A Review of the First Year of Research

Jeremy L. Praissman,
Lance Wells

Published online: June 02, 2021

100103

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Decoding Post-Translational Modification Crosstalk With Proteomics

Decoding Post-Translational Modification Crosstalk With Proteomics

Mario Leutert,
Samuel W. Entwisle,
Judit Villén

Published online: August 02, 2021

100129

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Uncovering the Depths of the Human Proteome: Antibody-based Technologies for Ultrasensitive Multiplexed Protein Detection and Quantification

Uncovering the Depths of the Human Proteome: Antibody-based Technologies for Ultrasensitive Multiplexed Protein Detection and Quantification

Annie H. Ren,
Eleftherios P. Diamandis,
Vathany Kulasingam

Published online: September 27, 2021

100155

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An Introduction to Advanced Targeted Acquisition Methods

An Introduction to Advanced Targeted Acquisition Methods

Mirjam van Bentum,
Matthias Selbach

Published online: October 18, 2021

100165

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Report

Asia-Oceania HUPO: Past, Present, and Future

Asia-Oceania HUPO: Past, Present, and Future

Yasushi Ishihama,
Yu-Ju Chen,
Je-Yoel Cho,
...
Teck Yew Low,
Terence Chuen Wai Poon,
Ho Jeong Kwon

Published online: January 16, 2021

100048

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Perspective

Ethical Principles, Constraints, and Opportunities in Clinical Proteomics

Ethical Principles, Constraints, and Opportunities in Clinical Proteomics

Sebastian Porsdam Mann,
Peter V. Treit,
Philipp E. Geyer,
Gilbert S. Omenn,
Matthias Mann

Published online: January 13, 2021

100046

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Reflections on the HUPO Human Proteome Project, the Flagship Project of the Human Proteome Organization, at 10 Years

Reflections on the HUPO Human Proteome Project, the Flagship Project of the Human Proteome Organization, at 10 Years

Gilbert S. Omenn

Published online: February 25, 2021

100062

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Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future

Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future

Nuno Bandeira,
Eric W. Deutsch,
Oliver Kohlbacher,
Lennart Martens,
Juan Antonio Vizcaíno

Published online: March 09, 2021

100071

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Trapped Ion Mobility Spectrometry and Parallel Accumulation–Serial Fragmentation in Proteomics

Trapped Ion Mobility Spectrometry and Parallel Accumulation–Serial Fragmentation in Proteomics

Florian Meier,
Melvin A. Park,
Matthias Mann

Published online: August 16, 2021

100138

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Research Article

Protein Modification Characteristics of the Malaria Parasite Plasmodium falciparum and the Infected Erythrocytes

Protein Modification Characteristics of the Malaria Parasite Plasmodium falciparum and the Infected Erythrocytes

Jianhua Wang,
Ning Jiang,
Xiaoyu Sang,
...
Ran Chen,
Xinyi Wang,
Qijun Chen

Published online: November 23, 2020

100001

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Proteome Analysis Reveals a Significant Host-Specific Response in Rhizobium leguminosarum bv. viciae Endosymbiotic Cells

Proteome Analysis Reveals a Significant Host-Specific Response in Rhizobium leguminosarum bv. viciae Endosymbiotic Cells

David Durán,
Marta Albareda,
Carlos García,
Ana-Isabel Marina,
Tomás Ruiz-Argüeso,
Jose-Manuel Palacios

Published online: December 06, 2020

100009

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Peptidomics-Driven Strategy Reveals Peptides and Predicted Proteases Associated With Oral Cancer Prognosis

Peptidomics-Driven Strategy Reveals Peptides and Predicted Proteases Associated With Oral Cancer Prognosis

Leandro Xavier Neves,
Daniela C. Granato,
Ariane Fidelis Busso-Lopes,
...
Luiz Paulo Kowalski,
Marcio Ajudarte Lopes,
Adriana F. Paes Leme

Published online: December 03, 2020

100004

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Proteogenomic Characterization of the Pathogenic Fungus Aspergillus flavus Reveals Novel Genes Involved in Aflatoxin Production

Proteogenomic Characterization of the Pathogenic Fungus Aspergillus flavus Reveals Novel Genes Involved in Aflatoxin Production

Mingkun Yang,
Zhuo Zhu,
Zhenhong Zhuang,
Youhuang Bai,
Shihua Wang,
Feng Ge

Published online: December 11, 2020

100013

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Quantitative Proteomics Reveals Association of Neuron Projection Development Genes ARF4, KIF5B, and RAB8A With Hirschsprung Disease

Quantitative Proteomics Reveals Association of Neuron Projection Development Genes ARF4, KIF5B, and RAB8A With Hirschsprung Disease

Qin Zhang,
Lihua Wu,
Baoling Bai,
...
Hui Wang,
Long Li,
Qian Jiang

Published online: December 07, 2020

100007

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Thyroglobulin Interactome Profiling Defines Altered Proteostasis Topology Associated With Thyroid Dyshormonogenesis

Thyroglobulin Interactome Profiling Defines Altered Proteostasis Topology Associated With Thyroid Dyshormonogenesis

Madison T. Wright,
Logan Kouba,
Lars Plate

Published online: December 07, 2020

100008

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Proteomic Identification of Coxiella burnetii Effector Proteins Targeted to the Host Cell Mitochondria During Infection

Proteomic Identification of Coxiella burnetii Effector Proteins Targeted to the Host Cell Mitochondria During Infection

Laura F. Fielden,
Nichollas E. Scott,
Catherine S. Palmer,
Chen Ai Khoo,
Hayley J. Newton,
Diana Stojanovski

Published online: December 03, 2020

100005

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A Proteomic Approach to Understand the Clinical Significance of Acute Myeloid Leukemia–Derived Extracellular Vesicles Reflecting Essential Characteristics of Leukemia

A Proteomic Approach to Understand the Clinical Significance of Acute Myeloid Leukemia–Derived Extracellular Vesicles Reflecting Essential Characteristics of Leukemia

Ka-Won Kang,
Hyoseon Kim,
Woojune Hur,
...
Kil Yeon Lee,
Kwang Pyo Kim,
Yong Park

Published online: December 07, 2020

100017

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On the Robustness of Graph-Based Clustering to Random Network Alterations

On the Robustness of Graph-Based Clustering to Random Network Alterations

R. Greg Stacey,
Michael A. Skinnider,
Leonard J. Foster

Published online: November 23, 2020

100002

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Thermal Proteome Profiling in Zebrafish Reveals Effects of Napabucasin on Retinoic Acid Metabolism

Thermal Proteome Profiling in Zebrafish Reveals Effects of Napabucasin on Retinoic Acid Metabolism

Niels M. Leijten,
Petra Bakker,
Herman P. Spaink,
Jeroen den Hertog,
Simone Lemeer

Published online: December 21, 2020

100033

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Prediction and Validation of Mouse Meiosis-Essential Genes Based on Spermatogenesis Proteome Dynamics

Prediction and Validation of Mouse Meiosis-Essential Genes Based on Spermatogenesis Proteome Dynamics

Kailun Fang,
Qidan Li,
Yu Wei,
...
Hui Yang,
Siqi Liu,
Charlie Degui Chen

Published online: January 05, 2021

100014

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The Mechanism of NEDD8 Activation of CUL5 Ubiquitin E3 Ligases

The Mechanism of NEDD8 Activation of CUL5 Ubiquitin E3 Ligases

Ryan J. Lumpkin,
Alla S. Ahmad,
Rachel Blake,
Christopher J. Condon,
Elizabeth A. Komives

Published online: January 05, 2021

100019

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Plasma Proteomes Can Be Reidentifiable and Potentially Contain Personally Sensitive and Incidental Findings

Plasma Proteomes Can Be Reidentifiable and Potentially Contain Personally Sensitive and Incidental Findings

Philipp E. Geyer,
Sebastian Porsdam Mann,
Peter V. Treit,
Matthias Mann

Published online: January 11, 2021

100035

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High-Throughput and Site-Specific N-Glycosylation Analysis of Human Alpha-1-Acid Glycoprotein Offers a Great Potential for New Biomarker Discovery

High-Throughput and Site-Specific N-Glycosylation Analysis of Human Alpha-1-Acid Glycoprotein Offers a Great Potential for New Biomarker Discovery

Toma Keser,
Marko Tijardović,
Ivan Gornik,
...
Gordan Lauc,
Olga Gornik,
Mislav Novokmet

Published online: January 22, 2021

100044

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In-Depth Characterization of the Staphylococcus aureus Phosphoproteome Reveals New Targets of Stk1

In-Depth Characterization of the Staphylococcus aureus Phosphoproteome Reveals New Targets of Stk1

Nadine Prust,
Saar van der Laarse,
Henk W.P. van den Toorn,
Nina M. van Sorge,
Simone Lemeer

Published online: January 11, 2021

100034

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Carboxylate-Modified Magnetic Bead (CMMB)-Based Isopropanol Gradient Peptide Fractionation (CIF) Enables Rapid and Robust Off-Line Peptide Mixture Fractionation in Bottom-Up Proteomics

Carboxylate-Modified Magnetic Bead (CMMB)-Based Isopropanol Gradient Peptide Fractionation (CIF) Enables Rapid and Robust Off-Line Peptide Mixture Fractionation in Bottom-Up Proteomics

Weixian Deng,
Jihui Sha,
Kathrin Plath,
James A. Wohlschlegel

Published online: January 18, 2021

100039

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A Potential Role for the Gsdf–eEF1α Complex in Inhibiting Germ Cell Proliferation: A Protein-Interaction Analysis in Medaka (Oryzias latipes) From a Proteomics Perspective

A Potential Role for the Gsdf–eEF1α Complex in Inhibiting Germ Cell Proliferation: A Protein-Interaction Analysis in Medaka (Oryzias latipes) From a Proteomics Perspective

Xinting Zhang,
Yuyang Chang,
Wanying Zhai,
...
Xiaomiao Zhao,
Liangbiao Chen,
Guijun Guan

Published online: January 07, 2021

100023

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Multisample Mass Spectrometry-Based Approach for Discovering Injury Markers in Chronic Kidney Disease

Multisample Mass Spectrometry-Based Approach for Discovering Injury Markers in Chronic Kidney Disease

Ji Eun Kim,
Dohyun Han,
Jin Seon Jeong,
...
Young Joo Kwon,
Yon Su Kim,
Seung Hee Yang

Published online: January 13, 2021

100037

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Interspecies Differences in Proteome Turnover Kinetics Are Correlated With Life Spans and Energetic Demands

Interspecies Differences in Proteome Turnover Kinetics Are Correlated With Life Spans and Energetic Demands

Kyle Swovick,
Denis Firsanov,
Kevin A. Welle,
...
Andrei Seluanov,
Vera Gorbunova,
Sina Ghaemmaghami

Published online: January 06, 2021

100041

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A Proteomics-Based Assessment of Inflammation Signatures in Endotoxemia

A Proteomics-Based Assessment of Inflammation Signatures in Endotoxemia

Sean A. Burnap,
Ursula Mayr,
Manu Shankar-Hari,
...
Ian Sabroe,
Robert F. Storey,
Manuel Mayr

Published online: December 21, 2020

100021

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Proteomic Analyses Identify Differentially Expressed Proteins and Pathways Between Low-Risk and High-Risk Subtypes of Early-Stage Lung Adenocarcinoma and Their Prognostic Impacts

Proteomic Analyses Identify Differentially Expressed Proteins and Pathways Between Low-Risk and High-Risk Subtypes of Early-Stage Lung Adenocarcinoma and Their Prognostic Impacts

Juntuo Zhou,
Bing Liu,
Zhongwu Li,
...
Xin Yang,
Lijun Zhong,
Nan Wu

Published online: January 25, 2021

100015

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Global Lysine Acetylation and 2-Hydroxyisobutyrylation Profiling Reveals the Metabolism Conversion Mechanism in Giardia lamblia

Global Lysine Acetylation and 2-Hydroxyisobutyrylation Profiling Reveals the Metabolism Conversion Mechanism in Giardia lamblia

Wenhe Zhu,
Xiaoming Jiang,
Hongyu Sun,
...
Di Liu,
Aixin Ma,
Xianmin Feng

Published online: January 07, 2021

100043

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Unraveling the MAX2 Protein Network in Arabidopsis thaliana: Identification of the Protein Phosphatase PAPP5 as a Novel MAX2 Interactor

Unraveling the MAX2 Protein Network in Arabidopsis thaliana: Identification of the Protein Phosphatase PAPP5 as a Novel MAX2 Interactor

Sylwia Struk,
Carolien De Cuyper,
Anse Jacobs,
...
Kris Gevaert,
Geert De Jaeger,
Sofie Goormachtig

Published online: January 06, 2021

100040

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Proteomic Analysis Uncovers Measles Virus Protein C Interaction With p65–iASPP Protein Complex

Proteomic Analysis Uncovers Measles Virus Protein C Interaction With p65–iASPP Protein Complex

Alice Meignié,
Chantal Combredet,
Marc Santolini,
...
Regis Grailhe,
Frédéric Tangy,
Anastassia V. Komarova

Published online: January 27, 2021

100049

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Systematic Identification of Plasmodium Falciparum Sporozoite Membrane Protein Interactions Reveals an Essential Role for the p24 Complex in Host Infection

Systematic Identification of Plasmodium Falciparum Sporozoite Membrane Protein Interactions Reveals an Essential Role for the p24 Complex in Host Infection

Julia Knöckel,
Kirsten Dundas,
Annie S.P. Yang,
...
Julian C. Rayner,
Oliver Billker,
Gavin J. Wright

Published online: January 27, 2021

100038

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Systematic Proteome and Lysine Succinylome Analysis Reveals Enhanced Cell Migration by Hyposuccinylation in Esophageal Squamous Cell Carcinoma

Systematic Proteome and Lysine Succinylome Analysis Reveals Enhanced Cell Migration by Hyposuccinylation in Esophageal Squamous Cell Carcinoma

Zhenchang Guo,
Feng Pan,
Liu Peng,
...
Liyan Xu,
Enmin Li,
Kai Zhang

Published online: February 06, 2021

100053

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Site-specific N-glycosylation Characterization of Recombinant SARS-CoV-2 Spike Proteins

Site-specific N-glycosylation Characterization of Recombinant SARS-CoV-2 Spike Proteins

Yong Zhang,
Wanjun Zhao,
Yonghong Mao,
...
Xiaofeng Lu,
Jingqiu Cheng,
Hao Yang

Published online: February 10, 2021

100058

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N-Glycomic Signature of Stage II Colorectal Cancer and Its Association With the Tumor Microenvironment

N-Glycomic Signature of Stage II Colorectal Cancer and Its Association With the Tumor Microenvironment

Fanny Boyaval,
René van Zeijl,
Hans Dalebout,
...
Hans Morreau,
Manfred Wuhrer,
Bram Heijs

Published online: February 10, 2021

100057

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Transcriptome and Secretome Analysis of Intra-Mammalian Life-Stages of Calicophoron daubneyi Reveals Adaptation to a Unique Host Environment

Transcriptome and Secretome Analysis of Intra-Mammalian Life-Stages of Calicophoron daubneyi Reveals Adaptation to a Unique Host Environment

Kathryn M. Huson,
Erwan Atcheson,
Nicola A.M. Oliver,
...
Sam Haldenby,
Steve Paterson,
Mark W. Robinson

Published online: February 10, 2021

100055

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Protein Phosphorylation in Depolarized Synaptosomes: Dissecting Primary Effects of Calcium from Synaptic Vesicle Cycling

Protein Phosphorylation in Depolarized Synaptosomes: Dissecting Primary Effects of Calcium from Synaptic Vesicle Cycling

Ivan Silbern,
Kuan-Ting Pan,
Maksims Fiosins,
...
Eugenio F. Fornasiero,
Henning Urlaub,
Reinhard Jahn

Published online: February 11, 2021

100061

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Identification of Novel Serological Autoantibodies in Takayasu Arteritis Patients Using HuProt Arrays

Identification of Novel Serological Autoantibodies in Takayasu Arteritis Patients Using HuProt Arrays

Xiaoting Wen,
Guang Song,
Chaojun Hu,
...
Jiang Qian,
Heng Zhu,
Yongzhe Li

Published online: February 02, 2021

100036

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New Proteomic Signatures to Distinguish Between Zika and Dengue Infections

New Proteomic Signatures to Distinguish Between Zika and Dengue Infections

Kristina Allgoewer,
Shuvadeep Maity,
Alice Zhao,
...
Hyungwon Choi,
Elodie Ghedin,
Christine Vogel

Published online: February 11, 2021

100052

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Antibody Binding Epitope Mapping (AbMap) of Hundred Antibodies in a Single Run

Antibody Binding Epitope Mapping (AbMap) of Hundred Antibodies in a Single Run

Huan Qi,
Mingliang Ma,
Chuansheng Hu,
...
Xiaodong Zhao,
Hua Li,
Sheng-ce Tao

Published online: February 10, 2021

100059

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Secretome and Comparative Proteomics of Yersinia pestis Identify Two Novel E3 Ubiquitin Ligases That Contribute to Plague Virulence

Secretome and Comparative Proteomics of Yersinia pestis Identify Two Novel E3 Ubiquitin Ligases That Contribute to Plague Virulence

Shiyang Cao,
Yuling Chen,
Yanfeng Yan,
...
Haiteng Deng,
Ruifu Yang,
Zongmin Du

Published online: February 21, 2021

100066

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Dynamic Changes to the Skeletal Muscle Proteome and Ubiquitinome Induced by the E3 Ligase, ASB2β

Dynamic Changes to the Skeletal Muscle Proteome and Ubiquitinome Induced by the E3 Ligase, ASB2β

Craig A. Goodman,
Jonathan R. Davey,
Adam Hagg,
Benjamin L. Parker,
Paul Gregorevic

Published online: January 28, 2021

100050

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Proximity-dependent Mapping of the Androgen Receptor Identifies Kruppel-like Factor 4 as a Functional Partner

Proximity-dependent Mapping of the Androgen Receptor Identifies Kruppel-like Factor 4 as a Functional Partner

Lauriane Vélot,
Frédéric Lessard,
Félix-Antoine Bérubé-Simard,
...
Steve Bilodeau,
Frédéric Pouliot,
Nicolas Bisson

Published online: February 25, 2021

100064

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Quantitative Proteomics and Phosphoproteomics Support a Role for Mut9-Like Kinases in Multiple Metabolic and Signaling Pathways in Arabidopsis

Quantitative Proteomics and Phosphoproteomics Support a Role for Mut9-Like Kinases in Multiple Metabolic and Signaling Pathways in Arabidopsis

Margaret E. Wilson,
Shin-Cheng Tzeng,
Megan M. Augustin,
...
Bradley S. Evans,
Toni M. Kutchan,
Dmitri A. Nusinow

Published online: March 04, 2021

100063

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Proteomic Profiling of Gastric Signet Ring Cell Carcinoma Tissues Reveals Characteristic Changes of the Complement Cascade Pathway

Proteomic Profiling of Gastric Signet Ring Cell Carcinoma Tissues Reveals Characteristic Changes of the Complement Cascade Pathway

Yang Fan,
Bin Bai,
Yuting Liang,
...
Fei Chen,
Qingchuan Zhao,
Siqi Liu

Published online: March 03, 2021

100068

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Mapping Isoform Abundance and Interactome of the Endogenous TMPRSS2-ERG Fusion Protein by Orthogonal Immunoprecipitation–Mass Spectrometry Assays

Mapping Isoform Abundance and Interactome of the Endogenous TMPRSS2-ERG Fusion Protein by Orthogonal Immunoprecipitation–Mass Spectrometry Assays

Zhiqiang Fu,
Yasmine Rais,
Tarek A. Bismar,
M. Eric Hyndman,
X. Chris Le,
Andrei P. Drabovich

Published online: March 22, 2021

100075

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Integrative Proteomic and Metabolomic Analysis Reveals Metabolic Phenotype in Mice With Cardiac-Specific Deletion of Natriuretic Peptide Receptor A

Integrative Proteomic and Metabolomic Analysis Reveals Metabolic Phenotype in Mice With Cardiac-Specific Deletion of Natriuretic Peptide Receptor A

Pan Chang,
Yan Niu,
Xiaomeng Zhang,
...
Xi Shen,
Baoying Chen,
Jun Yu

Published online: March 30, 2021

100072

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Feature Selection Methods for Protein Biomarker Discovery from Proteomics or Multiomics Data

Feature Selection Methods for Protein Biomarker Discovery from Proteomics or Multiomics Data

Zhiao Shi,
Bo Wen,
Qiang Gao,
Bing Zhang

Published online: April 19, 2021

100083

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Calculating Sample Size Requirements for Temporal Dynamics in Single-Cell Proteomics

Calculating Sample Size Requirements for Temporal Dynamics in Single-Cell Proteomics

Hannah Boekweg,
Amanda J. Guise,
Edward D. Plowey,
Ryan T. Kelly,
Samuel H. Payne

Published online: April 26, 2021

100085

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TMEM67, TMEM237, and Embigin in Complex With Monocarboxylate Transporter MCT1 Are Unique Components of the Photoreceptor Outer Segment Plasma Membrane

TMEM67, TMEM237, and Embigin in Complex With Monocarboxylate Transporter MCT1 Are Unique Components of the Photoreceptor Outer Segment Plasma Membrane

Nikolai P. Skiba,
Martha A. Cady,
Laurie Molday,
...
Nancy J. Philp,
Robert S. Molday,
Vadim Y. Arshavsky

Published online: April 29, 2021

100088

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Structural Investigations of Human A2M Identify a Hollow Native Conformation That Underlies Its Distinctive Protease-Trapping Mechanism

Structural Investigations of Human A2M Identify a Hollow Native Conformation That Underlies Its Distinctive Protease-Trapping Mechanism

Seandean Lykke Harwood,
Jeppe Lyngsø,
Alessandra Zarantonello,
...
Gregers Rom Andersen,
Jan Skov Pedersen,
Jan J. Enghild

Published online: May 05, 2021

100090

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The Expression of NTAL and Its Protein Interactors Is Associated With Clinical Outcomes in Acute Myeloid Leukemia

The Expression of NTAL and Its Protein Interactors Is Associated With Clinical Outcomes in Acute Myeloid Leukemia

Carolina Hassibe Thomé,
Germano Aguiar Ferreira,
Diego Antonio Pereira-Martins,
...
Jan Jacob Schuringa,
Eduardo M. Rego,
Vitor M. Faça

Published online: May 06, 2021

100091

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Adipose Triglyceride Lipase Loss Promotes a Metabolic Switch in A549 Non–Small Cell Lung Cancer Cell Spheroids

Adipose Triglyceride Lipase Loss Promotes a Metabolic Switch in A549 Non–Small Cell Lung Cancer Cell Spheroids

Sophie Honeder,
Tamara Tomin,
Laura Nebel,
...
Matthias Schittmayer,
Nassim Ghaffari-Tabrizi-Wizsy,
Ruth Birner-Gruenberger

Published online: May 13, 2021

100095

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Increased Wheat Protein Content via Introgression of an HMW Glutenin Selectively Reshapes the Grain Proteome

Increased Wheat Protein Content via Introgression of an HMW Glutenin Selectively Reshapes the Grain Proteome

Hui Cao,
Owen Duncan,
Shahidul Islam,
Jingjuan Zhang,
Wujun Ma,
A. Harvey Millar

Published online: May 14, 2021

100097

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Reverse Phase Protein Array Reveals Correlation of Retinoic Acid Metabolism With Cardiomyopathy in Friedreich's Ataxia

Reverse Phase Protein Array Reveals Correlation of Retinoic Acid Metabolism With Cardiomyopathy in Friedreich's Ataxia

Jill S. Napierala,
Kimal Rajapakshe,
Amanda Clark,
...
Dean P. Edwards,
Cristian Coarfa,
Marek Napierala

Published online: May 12, 2021

100094

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Proteomic Dissection of the Impact of Environmental Exposures on Mouse Seminal Vesicle Function

Proteomic Dissection of the Impact of Environmental Exposures on Mouse Seminal Vesicle Function

David A. Skerrett-Byrne,
Natalie A. Trigg,
Elizabeth G. Bromfield,
...
Sarah A. Robertson,
Brett Nixon,
John E. Schjenken

Published online: June 02, 2021

100107

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Quantitative Consequences of Protein Carriers in Immunopeptidomics and Tyrosine Phosphorylation MS2 Analyses

Quantitative Consequences of Protein Carriers in Immunopeptidomics and Tyrosine Phosphorylation MS² Analyses

Lauren E. Stopfer,
Jason E. Conage-Pough,
Forest M. White

Published online: May 27, 2021

100104

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Integrated Redox Proteomic Analysis Highlights New Mechanisms of Sensitivity to Silver Nanoparticles

Integrated Redox Proteomic Analysis Highlights New Mechanisms of Sensitivity to Silver Nanoparticles

Reetta Holmila,
Hanzhi Wu,
Jingyun Lee,
Allen W. Tsang,
Ravi Singh,
Cristina M. Furdui

Published online: March 20, 2021

100073

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The C-Mannosylome of Human Induced Pluripotent Stem Cells Implies a Role for ADAMTS16 C-Mannosylation in Eye Development

The C-Mannosylome of Human Induced Pluripotent Stem Cells Implies a Role for ADAMTS16 C-Mannosylation in Eye Development

Karsten Cirksena,
Hermann J. Hütte,
Aleksandra Shcherbakova,
...
Joachim Wittbrodt,
Hans Bakker,
Falk F.R. Buettner

Published online: May 08, 2021

100092

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Proteogenomic Assessment of Intraspecific Venom Variability: Molecular Adaptations in the Venom Arsenal of Conus purpurascens

Proteogenomic Assessment of Intraspecific Venom Variability: Molecular Adaptations in the Venom Arsenal of Conus purpurascens

Meghan Grandal,
Mickelene Hoggard,
Benjamin Neely,
W. Clay Davis,
Frank Marí

Published online: May 21, 2021

100100

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Normothermic Ex-vivo Kidney Perfusion in a Porcine Auto-Transplantation Model Preserves the Expression of Key Mitochondrial Proteins: An Unbiased Proteomics Analysis

Normothermic Ex-vivo Kidney Perfusion in a Porcine Auto-Transplantation Model Preserves the Expression of Key Mitochondrial Proteins: An Unbiased Proteomics Analysis

Caitriona M. McEvoy,
Sergi Clotet-Freixas,
Tomas Tokar,
...
Lisa A. Robinson,
Markus Selzner,
Ana Konvalinka

Published online: May 21, 2021

100101

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Revealing the Dynamic Allosteric Changes Required for Formation of the Cysteine Synthase Complex by Hydrogen-Deuterium Exchange MS

Revealing the Dynamic Allosteric Changes Required for Formation of the Cysteine Synthase Complex by Hydrogen-Deuterium Exchange MS

Brenda Rosa,
Eleanor R. Dickinson,
Marialaura Marchetti,
...
Barbara Pioselli,
Stefano Bettati,
Kasper Dyrberg Rand

Published online: May 19, 2021

100098

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Nuclear Phosphatidylinositol 3,4,5-Trisphosphate Interactome Uncovers an Enrichment in Nucleolar Proteins

Nuclear Phosphatidylinositol 3,4,5-Trisphosphate Interactome Uncovers an Enrichment in Nucleolar Proteins

Fatemeh Mazloumi Gavgani,
Malene Skuseth Slinning,
Andrea Papdiné Morovicz,
...
Sandra Ninzima,
Clive S. D’Santos,
Aurélia E. Lewis

Published online: May 25, 2021

100102

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Proteomic Portraits Reveal Evolutionarily Conserved and Divergent Responses to Spinal Cord Injury

Proteomic Portraits Reveal Evolutionarily Conserved and Divergent Responses to Spinal Cord Injury

Michael A. Skinnider,
Jason Rogalski,
Seth Tigchelaar,
...
Robert Balshaw,
Leonard J. Foster,
Brian K. Kwon

Published online: June 12, 2021

100096

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Deeply Mining a Universe of Peptides Encoded by Long Noncoding RNAs

Deeply Mining a Universe of Peptides Encoded by Long Noncoding RNAs

Qing Zhang,
Erzhong Wu,
Yiheng Tang,
...
Jianjun Luo,
Runsheng Chen,
Fuquan Yang

Published online: June 12, 2021

100109

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Age-Associated Proteomic Signatures and Potential Clinically Actionable Targets of Colorectal Cancer

Age-Associated Proteomic Signatures and Potential Clinically Actionable Targets of Colorectal Cancer

Yanqiu Gong,
Yu Liu,
Tian Wang,
...
Heng Xu,
Zongguang Zhou,
Lunzhi Dai

Published online: June 12, 2021

100115

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Proteome Profiling of Recombinant DNase Therapy in Reducing NETs and Aiding Recovery in COVID-19 Patients

Proteome Profiling of Recombinant DNase Therapy in Reducing NETs and Aiding Recovery in COVID-19 Patients

Jane Fisher,
Tirthankar Mohanty,
Christofer A.Q. Karlsson,
...
Pontus Nordenfelt,
Johan Malmstrom,
Adam Linder

Published online: June 14, 2021

100113

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Comparative Host Interactomes of the SARS-CoV-2 Nonstructural Protein 3 and Human Coronavirus Homologs

Comparative Host Interactomes of the SARS-CoV-2 Nonstructural Protein 3 and Human Coronavirus Homologs

Katherine M. Almasy,
Jonathan P. Davies,
Lars Plate

Published online: June 26, 2021

100120

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A Reductionist Approach Using Primary and Metastatic Cell–Derived Extracellular Vesicles Reveals Hub Proteins Associated with Oral Cancer Prognosis

A Reductionist Approach Using Primary and Metastatic Cell–Derived Extracellular Vesicles Reveals Hub Proteins Associated with Oral Cancer Prognosis

Ariane Fidelis Busso-Lopes,
Carolina Moretto Carnielli,
Flavia Vischi Winck,
...
Kelly Dryden,
Jay William Fox,
Adriana Franco Paes Leme

Published online: June 26, 2021

100118

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Proteome Characterization of Glaucoma Aqueous Humor

Proteome Characterization of Glaucoma Aqueous Humor

Xiaoyan Liu,
Xiang Liu,
Ying Wang,
...
Chengyan He,
Jiyu Xu,
Wei Sun

Published online: June 29, 2021

100117

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Unbiased Proteomic and Phosphoproteomic Analysis Identifies Response Signatures and Novel Susceptibilities After Combined MEK and mTOR Inhibition in BRAFV600E Mutant Glioma

Unbiased Proteomic and Phosphoproteomic Analysis Identifies Response Signatures and Novel Susceptibilities After Combined MEK and mTOR Inhibition in BRAF^V600E Mutant Glioma

Micah J. Maxwell,
Antje Arnold,
Heather Sweeney,
...
Hui Zhang,
David J. Clark,
Eric H. Raabe

Published online: July 20, 2021

100123

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Proteomic Landscape of Exosomes Reveals the Functional Contributions of CD151 in Triple-Negative Breast Cancer

Proteomic Landscape of Exosomes Reveals the Functional Contributions of CD151 in Triple-Negative Breast Cancer

Sipeng Li,
Xinya Li,
Siqi Yang,
...
Pingping Shen,
Xizhou Li,
Jianguo Ji

Published online: July 12, 2021

100121

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Quantitative Proteomic and Metabolomic Profiling Reveals Altered Mitochondrial Metabolism and Folate Biosynthesis Pathways in the Aging Drosophila Eye

Quantitative Proteomic and Metabolomic Profiling Reveals Altered Mitochondrial Metabolism and Folate Biosynthesis Pathways in the Aging Drosophila Eye

Hana Hall,
Bruce R. Cooper,
Guihong Qi,
Aruna B. Wijeratne,
Amber L. Mosley,
Vikki M. Weake

Published online: July 28, 2021

100127

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Proteomics, Lipidomics, Metabolomics, and 16S DNA Sequencing of Dental Plaque From Patients With Diabetes and Periodontal Disease

Proteomics, Lipidomics, Metabolomics, and 16S DNA Sequencing of Dental Plaque From Patients With Diabetes and Periodontal Disease

Katherine A. Overmyer,
Timothy W. Rhoads,
Anna E. Merrill,
...
Amit Acharya,
Sanjay K. Shukla,
Joshua J. Coon

Published online: July 28, 2021

100126

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Affinity Proteomics and Deglycoproteomics Uncover Novel EDEM2 Endogenous Substrates and an Integrative ERAD Network

Affinity Proteomics and Deglycoproteomics Uncover Novel EDEM2 Endogenous Substrates and an Integrative ERAD Network

Cristian V.A. Munteanu,
Gabriela N. Chirițoiu,
Marioara Chirițoiu,
Simona Ghenea,
Andrei-Jose Petrescu,
Ştefana M. Petrescu

Published online: July 28, 2021

100125

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Region-Specific Cell Membrane N-Glycome of Functional Mouse Brain Areas Revealed by nanoLC-MS Analysis

Region-Specific Cell Membrane N-Glycome of Functional Mouse Brain Areas Revealed by nanoLC-MS Analysis

Mariana Barboza,
Kemal Solakyildirim,
Trina A. Knotts,
...
Melanie G. Gareau,
Helen E. Raybould,
Carlito B. Lebrilla

Published online: August 03, 2021

100130

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Characterization of an A3G-VifHIV-1-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host–Pathogen Complexes

Characterization of an A3G-Vif_HIV-1-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host–Pathogen Complexes

Robyn M. Kaake,
Ignacia Echeverria,
Seung Joong Kim,
...
John Gross,
Andrej Sali,
Nevan J. Krogan

Published online: August 10, 2021

100132

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Proteomic Signature of Host Response to SARS-CoV-2 Infection in the Nasopharynx

Proteomic Signature of Host Response to SARS-CoV-2 Infection in the Nasopharynx

Patrick M. Vanderboom,
Dong-Gi Mun,
Anil K. Madugundu,
...
Hideki Ebihara,
Jie Sun,
Akhilesh Pandey

Published online: August 13, 2021

100134

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Decellularization Enables Characterization and Functional Analysis of Extracellular Matrix in Planarian Regeneration

Decellularization Enables Characterization and Functional Analysis of Extracellular Matrix in Planarian Regeneration

Ekasit Sonpho,
Frederick G. Mann Jr.,
Michaella Levy,
...
Viraj Doddihal,
Puey Ounjai,
Alejandro Sánchez Alvarado

Published online: August 17, 2021

100137

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Proteome Landscape of Epithelial-to-Mesenchymal Transition (EMT) of Retinal Pigment Epithelium Shares Commonalities With Malignancy-Associated EMT

Proteome Landscape of Epithelial-to-Mesenchymal Transition (EMT) of Retinal Pigment Epithelium Shares Commonalities With Malignancy-Associated EMT

Srinivasa R. Sripathi,
Ming-Wen Hu,
Ravi Chakra Turaga,
...
Cynthia A. Berlinicke,
Jiang Qian,
Donald J. Zack

Published online: August 26, 2021

100131

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Characterization of R-Loop–Interacting Proteins in Embryonic Stem Cells Reveals Roles in rRNA Processing and Gene Expression

Characterization of R-Loop–Interacting Proteins in Embryonic Stem Cells Reveals Roles in rRNA Processing and Gene Expression

Tong Wu,
Jennifer Nance,
Feixia Chu,
Thomas G. Fazzio

Published online: August 30, 2021

100142

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A Proteomic Study on the Membrane Protein Fraction of T Cells Confirms High Substrate Selectivity for the ER Translocation Inhibitor Cyclotriazadisulfonamide

A Proteomic Study on the Membrane Protein Fraction of T Cells Confirms High Substrate Selectivity for the ER Translocation Inhibitor Cyclotriazadisulfonamide

Eva Pauwels,
Claudia Rutz,
Becky Provinciael,
...
Heike Stephanowitz,
Ralf Schülein,
Kurt Vermeire

Published online: September 02, 2021

100144

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An Integrated Transcriptomics and Proteomics Analysis Implicates lncRNA MALAT1 in the Regulation of Lipid Metabolism

An Integrated Transcriptomics and Proteomics Analysis Implicates lncRNA MALAT1 in the Regulation of Lipid Metabolism

Hao Wang,
Yali Zhang,
Xinyu Guan,
...
Yan Gao,
Xiangyang Zhang,
Ruibing Chen

Published online: August 30, 2021

100141

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DeepHistoClass: A Novel Strategy for Confident Classification of Immunohistochemistry Images Using Deep Learning

DeepHistoClass: A Novel Strategy for Confident Classification of Immunohistochemistry Images Using Deep Learning

Biraja Ghoshal,
Feria Hikmet,
Charles Pineau,
Allan Tucker,
Cecilia Lindskog

Published online: August 20, 2021

100140

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Global Insights Into Lysine Acylomes Reveal Crosstalk Between Lysine Acetylation and Succinylation in Streptomyces coelicolor Metabolic Pathways

Global Insights Into Lysine Acylomes Reveal Crosstalk Between Lysine Acetylation and Succinylation in Streptomyces coelicolor Metabolic Pathways

Yujiao Yang,
Hong Zhang,
Zhenyang Guo,
...
Peng Li,
Guo-ping Zhao,
Wei Zhao

Published online: September 13, 2021

100148

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The Insufficient Activation of RIG-I–Like Signaling Pathway Contributes to Highly Efficient Replication of Porcine Picornaviruses in IBRS-2 Cells

The Insufficient Activation of RIG-I–Like Signaling Pathway Contributes to Highly Efficient Replication of Porcine Picornaviruses in IBRS-2 Cells

Xiangle Zhang,
Fan Yang,
Kangli Li,
...
Xiangtao Liu,
Zixiang Zhu,
Haixue Zheng

Published online: September 13, 2021

100147

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Sulfation of O-glycans on Mucin-type Proteins From Serous Ovarian Epithelial Tumors

Sulfation of O-glycans on Mucin-type Proteins From Serous Ovarian Epithelial Tumors

Kristina A. Thomsson,
Varvara Vitiazeva,
Constantina Mateoiu,
...
Birgitta Weijdegård,
Karin Sundfeldt,
Niclas G. Karlsson

Published online: September 20, 2021

100150

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Oxidative Modifications Switch Modulatory Activities of Urinary Proteins From Inhibiting to Promoting Calcium Oxalate Crystallization, Growth, and Aggregation

Oxidative Modifications Switch Modulatory Activities of Urinary Proteins From Inhibiting to Promoting Calcium Oxalate Crystallization, Growth, and Aggregation

Sakdithep Chaiyarit,
Visith Thongboonkerd

Published online: September 22, 2021

100151

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Assessing the Preanalytical Variability of Plasma and Cerebrospinal Fluid Processing and Its Effects on Inflammation-Related Protein Biomarkers

Assessing the Preanalytical Variability of Plasma and Cerebrospinal Fluid Processing and Its Effects on Inflammation-Related Protein Biomarkers

Jesse Huang,
Mohsen Khademi,
Örjan Lindhe,
...
Fredrik Piehl,
Tomas Olsson,
Ingrid Kockum

Published online: September 28, 2021

100157

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Pronounced Postmating Response in the Drosophila Female Reproductive Tract Fluid Proteome

Pronounced Postmating Response in the Drosophila Female Reproductive Tract Fluid Proteome

Caitlin E. McDonough-Goldstein,
Emma Whittington,
Erin L. McCullough,
...
Scott Erdman,
Scott Pitnick,
Steve Dorus

Published online: September 28, 2021

100156

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Metabolic Perturbation Associated With COVID-19 Disease Severity and SARS-CoV-2 Replication

Metabolic Perturbation Associated With COVID-19 Disease Severity and SARS-CoV-2 Replication

Shuba Krishnan,
Hampus Nordqvist,
Anoop T. Ambikan,
...
Anders Sönnerborg,
Carl Johan Treutiger,
Ujjwal Neogi

Published online: October 04, 2021

100159

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A Systematic Survey of the Light/Dark-dependent Protein Degradation Events in a Model Cyanobacterium

A Systematic Survey of the Light/Dark-dependent Protein Degradation Events in a Model Cyanobacterium

Weiyang Chen,
Limin Zheng,
Jinghui Dong,
...
Dandan Lu,
Wu Xu,
Yingchun Wang

Published online: October 13, 2021

100162

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Identification of SUMO Targets Associated With the Pluripotent State in Human Stem Cells

Identification of SUMO Targets Associated With the Pluripotent State in Human Stem Cells

Barbara Mojsa,
Michael H. Tatham,
Lindsay Davidson,
Magda Liczmanska,
Emma Branigan,
Ronald T. Hay

Published online: October 18, 2021

100164

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A Complex Proteomic Response of the Parasitic Nematode Anisakis simplex s.s. to Escherichia coli Lipopolysaccharide

A Complex Proteomic Response of the Parasitic Nematode Anisakis simplex s.s. to Escherichia coli Lipopolysaccharide

Karol Mierzejewski,
Robert Stryiński,
Elżbieta Łopieńska-Biernat,
Jesús Mateos,
Iwona Bogacka,
Mónica Carrera

Published online: October 18, 2021

100166

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Integrated Systems Analysis of the Murine and Human Pancreatic Cancer Glycomes Reveals a Tumor-Promoting Role for ST6GAL1

Integrated Systems Analysis of the Murine and Human Pancreatic Cancer Glycomes Reveals a Tumor-Promoting Role for ST6GAL1

Emma Kurz,
Shuhui Chen,
Emily Vucic,
...
Cristina Hajdu,
Dafna Bar-Sagi,
Lara K. Mahal

Published online: October 08, 2021

100160

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Proteogenomics Reveals Perturbed Signaling Networks in Malignant Melanoma Cells Resistant to BRAF Inhibition

Proteogenomics Reveals Perturbed Signaling Networks in Malignant Melanoma Cells Resistant to BRAF Inhibition

Marisa Schmitt,
Tobias Sinnberg,
Katrin Bratl,
...
Claus Garbe,
Boris Macek,
Nicolas C. Nalpas

Published online: October 18, 2021

100163

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Deep-Learning-Derived Evaluation Metrics Enable Effective Benchmarking of Computational Tools for Phosphopeptide Identification

Deep-Learning-Derived Evaluation Metrics Enable Effective Benchmarking of Computational Tools for Phosphopeptide Identification

Wen Jiang,
Bo Wen,
Kai Li,
...
Tao Liu,
Alexey I. Nesvizhskii,
Bing Zhang

Published online: November 01, 2021

100171

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Quantitative Ubiquitylome Analysis Reveals the Specificity of RNF111/Arkadia E3 Ubiquitin Ligase for its Degradative Substrates SKI and SKIL/SnoN in TGF-β Signaling Pathway

Quantitative Ubiquitylome Analysis Reveals the Specificity of RNF111/Arkadia E3 Ubiquitin Ligase for its Degradative Substrates SKI and SKIL/SnoN in TGF-β Signaling Pathway

Victor Laigle,
Florent Dingli,
Sadek Amhaz,
...
Damarys Loew,
Céline Prunier,
Laurence Levy

Published online: November 02, 2021

100173

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Technological Innovation and Resources

Spectral Prediction Features as a Solution for the Search Space Size Problem in Proteogenomics

Spectral Prediction Features as a Solution for the Search Space Size Problem in Proteogenomics

Steven Verbruggen,
Siegfried Gessulat,
Ralf Gabriels,
...
Wim Van Criekinge,
Mathias Wilhelm,
Gerben Menschaert

Published online: April 02, 2021

100076

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Feasibility of Phosphoproteomics on Leftover Samples After RNA Extraction With Guanidinium Thiocyanate

Feasibility of Phosphoproteomics on Leftover Samples After RNA Extraction With Guanidinium Thiocyanate

Frank Rolfs,
Sander R. Piersma,
Mariana Paes Dias,
Jos Jonkers,
Connie R. Jimenez

Published online: April 02, 2021

100078

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Isolation of Acetylated and Unmodified Protein N-Terminal Peptides by Strong Cation Exchange Chromatographic Separation of TrypN-Digested Peptides

Isolation of Acetylated and Unmodified Protein N-Terminal Peptides by Strong Cation Exchange Chromatographic Separation of TrypN-Digested Peptides

Chih-Hsiang Chang,
Hsin-Yi Chang,
Juri Rappsilber,
Yasushi Ishihama

Published online: November 23, 2020

100003

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PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results

PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results

Daniel J. Geiszler,
Andy T. Kong,
Dmitry M. Avtonomov,
Fengchao Yu,
Felipe da Veiga Leprevost,
Alexey I. Nesvizhskii

Published online: December 10, 2020

100018

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Blockade of High-Fat Diet Proteomic Phenotypes Using Exercise as Prevention or Treatment

Blockade of High-Fat Diet Proteomic Phenotypes Using Exercise as Prevention or Treatment

Sergio F. Martinez-Huenchullan,
Isaac Shipsey,
Luke Hatchwell,
Danqing Min,
Stephen M. Twigg,
Mark Larance

Published online: December 18, 2020

100027

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SCASP: A Simple and Robust SDS-Aided Sample Preparation Method for Proteomic Research

SCASP: A Simple and Robust SDS-Aided Sample Preparation Method for Proteomic Research

Guohong Gan,
Xiao Xu,
Xi Chen,
Xiu-Fang Zhang,
Jinling Wang,
Chuan-Qi Zhong

Published online: February 04, 2021

100051

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Stable Isotope Labeling of Amino Acids in Flies (SILAF) Reveals Differential Phosphorylation of Mitochondrial Proteins Upon Loss of OXPHOS Subunits

Stable Isotope Labeling of Amino Acids in Flies (SILAF) Reveals Differential Phosphorylation of Mitochondrial Proteins Upon Loss of OXPHOS Subunits

Florian A. Rosenberger,
Ilian Atanassov,
David Moore,
...
Anna Wedell,
Christoph Freyer,
Anna Wredenberg

Published online: February 25, 2021

100065

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Quantifying Positional Isomers (QPI) by Top-Down Mass Spectrometry

Quantifying Positional Isomers (QPI) by Top-Down Mass Spectrometry

Andrea M. Brunner,
Philip Lössl,
Paul P. Geurink,
...
A.F. Maarten Altelaar,
Albert J.R. Heck,
Richard A. Scheltema

Published online: March 09, 2021

100070

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Evaluation and Refinement of Sample Preparation Methods for Extracellular Matrix Proteome Coverage

Evaluation and Refinement of Sample Preparation Methods for Extracellular Matrix Proteome Coverage

Maxwell C. McCabe,
Lauren R. Schmitt,
Ryan C. Hill,
...
Toin H. van Kuppevelt,
Danique J. Hof,
Kirk C. Hansen

Published online: April 09, 2021

100079

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IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs

IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs

Fengchao Yu,
Sarah E. Haynes,
Alexey I. Nesvizhskii

Published online: April 01, 2021

100077

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A Chemical Acetylation-Based Mass Spectrometry Platform for Histone Methylation Profiling

A Chemical Acetylation-Based Mass Spectrometry Platform for Histone Methylation Profiling

Francesca Zappacosta,
Craig D. Wagner,
Anthony Della Pietra III,
...
Olena Barbash,
Michael T. McCabe,
Roland S. Annan

Published online: March 25, 2021

100067

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A New Parallel High-Pressure Packing System Enables Rapid Multiplexed Production of Capillary Columns

A New Parallel High-Pressure Packing System Enables Rapid Multiplexed Production of Capillary Columns

Johannes B. Müller-Reif,
Fynn M. Hansen,
Lisa Schweizer,
Peter V. Treit,
Philipp E. Geyer,
Matthias Mann

Published online: April 19, 2021

100082

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Enabling Photoactivated Cross-Linking Mass Spectrometric Analysis of Protein Complexes by Novel MS-Cleavable Cross-Linkers

Enabling Photoactivated Cross-Linking Mass Spectrometric Analysis of Protein Complexes by Novel MS-Cleavable Cross-Linkers

Craig Gutierrez,
Leah J. Salituro,
Clinton Yu,
...
Sadie F. DePeter,
Scott D. Rychnovsky,
Lan Huang

Published online: April 26, 2021

100084

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GAGrank: Software for Glycosaminoglycan Sequence Ranking Using a Bipartite Graph Model

GAGrank: Software for Glycosaminoglycan Sequence Ranking Using a Bipartite Graph Model

John D. Hogan,
Jiandong Wu,
Joshua A. Klein,
Cheng Lin,
Luis Carvalho,
Joseph Zaia

Published online: May 13, 2021

100093

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Trimethylacetic Anhydride–Based Derivatization Facilitates Quantification of Histone Marks at the MS1 Level

Trimethylacetic Anhydride–Based Derivatization Facilitates Quantification of Histone Marks at the MS1 Level

Hana Kuchaříková,
Pavlína Dobrovolná,
Gabriela Lochmanová,
Zbyněk Zdráhal

Published online: June 12, 2021

100114

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Identification of Endogenous Kinase Substrates by Proximity Labeling Combined with Kinase Perturbation and Phosphorylation Motifs

Identification of Endogenous Kinase Substrates by Proximity Labeling Combined with Kinase Perturbation and Phosphorylation Motifs

Tomoya Niinae,
Koshi Imami,
Naoyuki Sugiyama,
Yasushi Ishihama

Published online: June 26, 2021

100119

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A Toolbox for Efficient Proximity-Dependent Biotinylation in Zebrafish Embryos

A Toolbox for Efficient Proximity-Dependent Biotinylation in Zebrafish Embryos

Shimon M. Rosenthal,
Tvisha Misra,
Hala Abdouni,
...
Alice Y. Ting,
Ian C. Scott,
Anne-Claude Gingras

Published online: July 28, 2021

100128

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IMProv: A Resource for Cross-link-Driven Structure Modeling that Accommodates Protein Dynamics

IMProv: A Resource for Cross-link-Driven Structure Modeling that Accommodates Protein Dynamics

Daniel S. Ziemianowicz,
Daniel Saltzberg,
Troy Pells,
...
Morgan Hepburn,
Andrej Sali,
David C. Schriemer

Published online: August 18, 2021

100139

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A Universal Peptide Matrix Interactomics Approach to Disclose Motif-Dependent Protein Binding

A Universal Peptide Matrix Interactomics Approach to Disclose Motif-Dependent Protein Binding

Evelyn Ramberger,
Lorena Suarez-Artiles,
Daniel Perez-Hernandez,
...
Achim Leutz,
Gunnar Dittmar,
Philipp Mertins

Published online: August 12, 2021

100135

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AlphaTims: Indexing Trapped Ion Mobility Spectrometry–TOF Data for Fast and Easy Accession and Visualization

AlphaTims: Indexing Trapped Ion Mobility Spectrometry–TOF Data for Fast and Easy Accession and Visualization

Sander Willems,
Eugenia Voytik,
Patricia Skowronek,
Maximilian T. Strauss,
Matthias Mann

Published online: September 17, 2021

100149

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Automating UbiFast for High-throughput and Multiplexed Ubiquitin Enrichment

Automating UbiFast for High-throughput and Multiplexed Ubiquitin Enrichment

Keith D. Rivera,
Meagan E. Olive,
Erik J. Bergstrom,
...
Shankha Satpathy,
Steven A. Carr,
Namrata D. Udeshi

Published online: September 27, 2021

100154

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Novel Antibodies for the Simple and Efficient Enrichment of Native O-GlcNAc Modified Peptides

Novel Antibodies for the Simple and Efficient Enrichment of Native O-GlcNAc Modified Peptides

Rajan A. Burt,
Borislav Dejanovic,
Hayley J. Peckham,
...
Stacy A. Malaker,
Steven A. Carr,
Samuel A. Myers

Published online: October 19, 2021

100167

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Proximity Extension Assay in Combination with Next-Generation Sequencing for High-throughput Proteome-wide Analysis

Proximity Extension Assay in Combination with Next-Generation Sequencing for High-throughput Proteome-wide Analysis

Lotta Wik,
Niklas Nordberg,
John Broberg,
...
Elin Liljeroth,
Adam Falck,
Martin Lundberg

Published online: October 26, 2021

100168

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CoolTip: Low-Temperature Solid-Phase Extraction Microcolumn for Capturing Hydrophilic Peptides and Phosphopeptides

CoolTip: Low-Temperature Solid-Phase Extraction Microcolumn for Capturing Hydrophilic Peptides and Phosphopeptides

Kosuke Ogata,
Yasushi Ishihama

Published online: November 02, 2021

100170

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Supplemental Materials

Special Issue: Glycoproteomics

Editorial

Glycoproteomics: Making the Study of the Most Structurally Diverse and Most Abundant Post-Translational Modifications More Accessible to the Scientific Community

Gerald W. Hart,
Lance Wells

Published online: June 03, 2021

100086

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Research Article

The Complexity and Dynamics of the Tissue Glycoproteome Associated With Prostate Cancer Progression

The Complexity and Dynamics of the Tissue Glycoproteome Associated With Prostate Cancer Progression

Rebeca Kawahara,
Saulo Recuero,
Miguel Srougi,
Katia R.M. Leite,
Morten Thaysen-Andersen,
Giuseppe Palmisano

Published online: January 04, 2021

100026

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Peak Filtering, Peak Annotation, and Wildcard Search for Glycoproteomics

Peak Filtering, Peak Annotation, and Wildcard Search for Glycoproteomics

Abhishek Roushan,
Gary M. Wilson,
Doron Kletter,
...
Yong J. Kil,
Eric Carlson,
Marshall Bern

Published online: December 07, 2020

100011

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Imaging Mass Spectrometry and Lectin Analysis of N-Linked Glycans in Carbohydrate Antigen–Defined Pancreatic Cancer Tissues

Imaging Mass Spectrometry and Lectin Analysis of N-Linked Glycans in Carbohydrate Antigen–Defined Pancreatic Cancer Tissues

Colin T. McDowell,
Zachary Klamer,
Johnathan Hall,
...
David N. Lewin,
Brian B. Haab,
Richard R. Drake

Published online: December 07, 2020

100012

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Integrated Glycoproteomics Identifies a Role of N-Glycosylation and Galectin-1 on Myogenesis and Muscle Development

Integrated Glycoproteomics Identifies a Role of N-Glycosylation and Galectin-1 on Myogenesis and Muscle Development

Ronnie Blazev,
Christopher Ashwood,
Jodie L. Abrahams,
...
Paul Gregorevic,
Morten Thaysen-Andersen,
Benjamin L. Parker

Published online: December 18, 2020

100030

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Quantitative Data-Independent Acquisition Glycoproteomics of Sparkling Wine

Quantitative Data-Independent Acquisition Glycoproteomics of Sparkling Wine

Cassandra L. Pegg,
Toan K. Phung,
Christopher H. Caboche,
...
Marshall Bern,
Kate Howell,
Benjamin L. Schulz

Published online: December 21, 2020

100020

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Separation and Identification of Permethylated Glycan Isomers by Reversed Phase NanoLC-NSI-MSn

Separation and Identification of Permethylated Glycan Isomers by Reversed Phase NanoLC-NSI-MSⁿ

Simone Kurz,
M. Osman Sheikh,
Shan Lu,
Lance Wells,
Michael Tiemeyer

Published online: January 25, 2021

100045

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Domain Mapping of Chondroitin/Dermatan Sulfate Glycosaminoglycans Enables Structural Characterization of Proteoglycans

Domain Mapping of Chondroitin/Dermatan Sulfate Glycosaminoglycans Enables Structural Characterization of Proteoglycans

Andrea Persson,
Mahnaz Nikpour,
Egor Vorontsov,
Jonas Nilsson,
Göran Larson

Published online: March 20, 2021

100074

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Quantitative Proteomics Reveals that the OGT Interactome Is Remodeled in Response to Oxidative Stress

Quantitative Proteomics Reveals that the OGT Interactome Is Remodeled in Response to Oxidative Stress

Marissa Martinez,
Santosh Renuse,
Simion Kreimer,
...
Robert Cole,
Akhilesh Pandey,
Natasha E. Zachara

Published online: March 11, 2021

100069

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In-depth Site-specific Analysis of N-glycoproteome in Human Cerebrospinal Fluid and Glycosylation Landscape Changes in Alzheimer's Disease

In-depth Site-specific Analysis of N-glycoproteome in Human Cerebrospinal Fluid and Glycosylation Landscape Changes in Alzheimer's Disease

Zhengwei Chen,
Qinying Yu,
Qing Yu,
...
Cynthia Carlsson,
Ozioma Okonkwo,
Lingjun Li

Published online: April 13, 2021

100081

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Review

Methods for Enrichment and Assignment of N-Acetylglucosamine Modification Sites

Methods for Enrichment and Assignment of N-Acetylglucosamine Modification Sites

Jason C. Maynard,
Robert J. Chalkley

Published online: December 19, 2020

100031

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Meta-heterogeneity: Evaluating and Describing the Diversity in Glycosylation Between Sites on the Same Glycoprotein

Meta-heterogeneity: Evaluating and Describing the Diversity in Glycosylation Between Sites on the Same Glycoprotein

Tomislav Čaval,
Albert J.R. Heck,
Karli R. Reiding

Published online: December 07, 2020

100010

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A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry–Based Glycoproteomics

A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry–Based Glycoproteomics

Nicholas M. Riley,
Carolyn R. Bertozzi,
Sharon J. Pitteri

Published online: December 19, 2020

100029

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The Role of Data-Independent Acquisition for Glycoproteomics

The Role of Data-Independent Acquisition for Glycoproteomics

Zilu Ye,
Sergey Y. Vakhrushev

Published online: January 06, 2021

100042

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Glycomics, Glycoproteomics, and Glycogenomics: An Inter-Taxa Evolutionary Perspective

Glycomics, Glycoproteomics, and Glycogenomics: An Inter-Taxa Evolutionary Perspective

Christopher M. West,
Daniel Malzl,
Alba Hykollari,
Iain B.H. Wilson

Published online: January 05, 2021

100024

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Calculating Glycoprotein Similarities From Mass Spectrometric Data

Calculating Glycoprotein Similarities From Mass Spectrometric Data

William E. Hackett,
Joseph Zaia

Published online: January 05, 2021

100028

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Developments in Mass Spectrometry for Glycosaminoglycan Analysis: A Review

Developments in Mass Spectrometry for Glycosaminoglycan Analysis: A Review

Lauren E. Pepi,
Patience Sanderson,
Morgan Stickney,
I. Jonathan Amster

Published online: January 05, 2021

100025

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Recent Advances in Software Tools for More Generic and Precise Intact Glycopeptide Analysis

Recent Advances in Software Tools for More Generic and Precise Intact Glycopeptide Analysis

Weiqian Cao,
Mingqi Liu,
Siyuan Kong,
Mengxi Wu,
Yang Zhang,
Pengyuan Yang

Published online: February 05, 2021

100060

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Recent Advances in Analytical Approaches for Glycan and Glycopeptide Quantitation

Recent Advances in Analytical Approaches for Glycan and Glycopeptide Quantitation

Daniel G. Delafield,
Lingjun Li

Published online: February 19, 2021

100054

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Special Issue: Immunopeptidomics

Research Article

CIITA-Transduced Glioblastoma Cells Uncover a Rich Repertoire of Clinically Relevant Tumor-Associated HLA-II Antigens

CIITA-Transduced Glioblastoma Cells Uncover a Rich Repertoire of Clinically Relevant Tumor-Associated HLA-II Antigens

Greta Forlani,
Justine Michaux,
HuiSong Pak,
...
Michael Linnebacher,
Roberto S. Accolla,
Michal Bassani-Sternberg

Published online: January 05, 2021

100032

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HLA Class II Presentation Is Specifically Altered at Elevated Temperatures in the B-Lymphoblastic Cell Line JY

HLA Class II Presentation Is Specifically Altered at Elevated Temperatures in the B-Lymphoblastic Cell Line JY

Laura C. Demmers,
Wei Wu,
Albert J.R. Heck

Published online: April 29, 2021

100089

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The Effect of Interferons on Presentation of Defective Ribosomal Products as HLA Peptides

The Effect of Interferons on Presentation of Defective Ribosomal Products as HLA Peptides

Liran Komov,
Dganit Melamed Kadosh,
Eilon Barnea,
Arie Admon

Published online: May 31, 2021

100105

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Allele-Specific Thresholds of Eluted Ligands for T-Cell Epitope Prediction

Allele-Specific Thresholds of Eluted Ligands for T-Cell Epitope Prediction

Brian Reardon,
Zeynep Koşaloğlu-Yalçın,
Sinu Paul,
Bjoern Peters,
Alessandro Sette

Published online: July 21, 2021

100122

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The Choice of Search Engine Affects Sequencing Depth and HLA Class I Allele-Specific Peptide Repertoires

The Choice of Search Engine Affects Sequencing Depth and HLA Class I Allele-Specific Peptide Repertoires

Robert Parker,
Arun Tailor,
Xu Peng,
...
Holger Wenschuh,
Karsten Schnatbaum,
Nicola Ternette

Published online: July 22, 2021

100124

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Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma

Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma

Yue A. Qi,
Tapan K. Maity,
Constance M. Cultraro,
...
Cenk Sahinalp,
James C. Yang,
Udayan Guha

Published online: August 12, 2021

100136

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Review

The Peptide Vaccine of the Future

The Peptide Vaccine of the Future

Annika Nelde,
Hans-Georg Rammensee,
Juliane S. Walz

Published online: December 21, 2020

100022

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MHC Phosphopeptides: Promising Targets for Immunotherapy of Cancer and Other Chronic Diseases

MHC Phosphopeptides: Promising Targets for Immunotherapy of Cancer and Other Chronic Diseases

Keira E. Mahoney,
Jeffrey Shabanowitz,
Donald F. Hunt

Published online: June 11, 2021

100112

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MS-Based HLA-II Peptidomics Combined With Multiomics Will Aid the Development of Future Immunotherapies

MS-Based HLA-II Peptidomics Combined With Multiomics Will Aid the Development of Future Immunotherapies

Hannah B. Taylor,
Susan Klaeger,
Karl R. Clauser,
...
Daniel B. Graham,
Steven A. Carr,
Jennifer G. Abelin

Published online: June 15, 2021

100116

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Technological Innovation and Resources

Sensitive Immunopeptidomics by Leveraging Available Large-Scale Multi-HLA Spectral Libraries, Data-Independent Acquisition, and MS/MS Prediction

Sensitive Immunopeptidomics by Leveraging Available Large-Scale Multi-HLA Spectral Libraries, Data-Independent Acquisition, and MS/MS Prediction

HuiSong Pak,
Justine Michaux,
Florian Huber,
...
Markus Müller,
George Coukos,
Michal Bassani-Sternberg

Published online: April 09, 2021

100080

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Sensitive and Quantitative Detection of MHC-I Displayed Neoepitopes Using a Semiautomated Workflow and TOMAHAQ Mass Spectrometry

Sensitive and Quantitative Detection of MHC-I Displayed Neoepitopes Using a Semiautomated Workflow and TOMAHAQ Mass Spectrometry

Samuel B. Pollock,
Christopher M. Rose,
Martine Darwish,
...
Lélia Delamarre,
Craig Blanchette,
Jennie R. Lill

Published online: June 12, 2021

100108

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Optimized Liquid and Gas Phase Fractionation Increases HLA-Peptidome Coverage for Primary Cell and Tissue Samples

Optimized Liquid and Gas Phase Fractionation Increases HLA-Peptidome Coverage for Primary Cell and Tissue Samples

Susan Klaeger,
Annie Apffel,
Karl R. Clauser,
...
Derin B. Keskin,
Catherine J. Wu,
Steven A. Carr

Published online: August 11, 2021

100133

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Pitfalls in HLA Ligandomics—How to Catch a Li(e)gand

Pitfalls in HLA Ligandomics—How to Catch a Li(e)gand

Jens Fritsche,
Daniel J. Kowalewski,
Linus Backert,
...
Heiko Schuster,
Oliver Schoor,
Toni Weinschenk

Published online: June 12, 2021

100110

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Precision Neoantigen Discovery Using Large-scale Immunopeptidomes and Composite Modeling of MHC Peptide Presentation

Rachel Marty Pyke,
Dattatreya Mellacheruvu,
Steven Dea,
...
Michael P. Snyder,
Richard Chen,
Sean Michael Boyle

Published online: June 11, 2021

100111

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Immunopeptidogenomics: Harnessing RNA-Seq to Illuminate the Dark Immunopeptidome

Immunopeptidogenomics: Harnessing RNA-Seq to Illuminate the Dark Immunopeptidome

Katherine E. Scull,
Kirti Pandey,
Sri H. Ramarathinam,
Anthony W. Purcell

Published online: September 09, 2021

100143

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Perspective

Are There Indeed Spliced Peptides in the Immunopeptidome?

Are There Indeed Spliced Peptides in the Immunopeptidome?

Arie Admon

Published online: May 19, 2021

100099

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Commentary

Commentary: Are There Indeed Spliced Peptides in the Immunopeptidome?

Commentary: Are There Indeed Spliced Peptides in the Immunopeptidome?

Michele Mishto

Published online: October 01, 2021

100158

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