Longitudinal proteomic profiling provides insights into host response and proteome dynamics in COVID ‐19 progression
This study also identified potential biomarkers that could be further validated, which may support better predicting and monitoring progression to severe COVID‐19.This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - May 5, 2021 Category: Biochemistry Authors: Jee ‐Soo Lee, Dohyun Han, So Yeon Kim, Ki Ho Hong, Myoung‐jin Jang, Man Jin Kim, Young‐gon Kim, Jae Hyeon Park, Sung Im Cho, Wan Beom Park, Kyung Bok Lee, Ho Seob Shin, Hyeon Sae Oh, Taek Soo Kim, Sung Sup Park, Moon‐Woo Seong Tags: RESEARCH ARTICLE Source Type: research

Proteomic analyses reveal that immune integrins are major targets for regulation by Membrane ‐Associated Ring‐CH (MARCH) proteins MARCH2,3,4 and 9
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - May 4, 2021 Category: Biochemistry Authors: Jarrod J Sandow, Andrew I Webb, Dina Stockwell, Nadia J Kershaw, Cyrus Tan, Satoshi Ishido, Warren S Alexander, Douglas J Hilton, Jeffrey J Babon, Nicos A Nicola Tags: Research Article Source Type: research

Extracellular vesicles in the transfusion medicine field: The potential of proteomics
AbstractIn transfusion centres, blood components are divided and stored following specific guidelines. The storage temperature and time vary among the blood cells but all of them release extracellular vesicles (EVs) under blood bank conditions. The clinical impact of such vesicles in blood components for transfusion is an object of debate, but should be considered and is being investigated. In this context, proteomics is an excellent tool to study the cargo and composition of EVs derived from red blood cells and platelets, since such vesicles are enriched in lipids and proteins. The development of quantitative mass spectro...
Source: Proteomics - May 4, 2021 Category: Biochemistry Authors: Lidia Hermida ‐Nogueira, Ángel García Tags: Viewpoint Source Type: research

Standard abbreviations
(Source: Proteomics)
Source: Proteomics - May 4, 2021 Category: Biochemistry Tags: STANDARD ABBREVIATIONS Source Type: research

Front Cover
Cover Image © Wiley‐VCH GmbH. The image is part of a figure in the article DOI:10.1002/pmic.201900203by Lei Li, Yong Jiang et al. (Source: Proteomics)
Source: Proteomics - May 3, 2021 Category: Biochemistry Tags: FRONT COVER Source Type: research

Contents: Proteomics 9'21
(Source: Proteomics)
Source: Proteomics - May 3, 2021 Category: Biochemistry Tags: CONTENTS Source Type: research

Editorial Board: Proteomics 9'21
(Source: Proteomics)
Source: Proteomics - May 3, 2021 Category: Biochemistry Tags: EDITORIAL BOARD Source Type: research

Understanding extracellular vesicle and nanoparticle heterogeneity: Novel methods and considerations
AbstractExtracellular vesicles (EVs) are a heterogeneous population of membrane ‐enclosed nanoparticles released by cells. They play a role in intercellular communication and are involved in numerous physiological and pathological processes. Cells release subpopulations of EVs with distinct composition and inherent biological function which overlap in size. Current size‐bas ed isolation methods are, therefore, not optimal to discriminate between functional EV subpopulations. In addition, EVs overlap in size with several other biological nanoparticles, such as lipoproteins and viruses. Proteomic analysis has allowed for...
Source: Proteomics - May 3, 2021 Category: Biochemistry Authors: William Phillips, Eduard Willms, Andrew F. Hill Tags: Review Source Type: research

Label ‐free quantitative proteomic analysis of extracellular vesicles released from fibroblasts derived from patients with spinal muscular atrophy
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - April 24, 2021 Category: Biochemistry Authors: Justin Roberto, Kathy L. Poulin, Robin J. Parks, Panayiotis O. Vacratsis Tags: RESEARCH ARTICLE Source Type: research

A Tandem Mass Tags (TMTs) labeling approach highlights differences between the shoot proteome of two Arabidopsis thaliana ecotypes, Col ‐0 and Ws
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - April 23, 2021 Category: Biochemistry Authors: Ma ïté Leschevin, Paulo Marcelo, Marwa Ismael, Hélène San‐Clemente, Elisabeth Jamet, Catherine Rayon, Karine Pageau Tags: DATASET BRIEF Source Type: research

Membrane to Cytosol Redistribution of αII‐Spectrin Drives Extracellular vesicle Biogenesis in Malignant Breast Cells
This study aims to examine the role of αII‐spectrin in malignant and non‐malignant plasma membrane vesiculation. We developed a custom, automated cell segmentation plugin for the image processor, Fiji, that provides an unbiased assessment of high resolution confocal microscopy images of the subcellular distribution of αII‐spectrin. We show that, in low vesiculating non‐malignant MBE‐F breast cells, prominent cortical spectrin localises to the cell periphery at rest. In comparison, cortical spectrin is dimin ished in high vesiculating malignant MCF‐7 breast cells at rest. A cortical distribution of s...
Source: Proteomics - April 19, 2021 Category: Biochemistry Authors: Taylor Jack, Patio Kevin, De Rubis Gabriele, Morris M.B, Evenhuis Christian, Johnson Michael, Mary Bebawy Tags: Research Article Source Type: research

Proteome characterisation of extracellular vesicles isolated from heart
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - April 16, 2021 Category: Biochemistry Authors: Bethany Claridge, Alin Rai, Haoyun Fang, Aya Matsumoto, Jieting Luo, Julie R McMullen, David W Greening Tags: Dataset Brief Source Type: research

Mass spectrometry ‐based proteomic platforms for better understanding of SARS‐CoV‐2 induced pathogenesis and potential diagnostic approaches
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - April 16, 2021 Category: Biochemistry Authors: Nagib Ahsan, R Shyama Prasad Rao, Rashaun S Wilson, Ujwal Punyamurtula, Fernanda Salvato, Max Petersen, Mohammad Kabir Ahmed, M Ruhul Abid, Jacob C. Verburgt, Daisuke Kihara, Zhibo Yang, Luca Fornelli, Steven B Foster, Bharat Ramratnam Tags: Review Source Type: research

Proteome reprogramming of endometrial epithelial cells by human trophectodermal small extracellular vesicles reveals key insights into embryo implantation
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - April 16, 2021 Category: Biochemistry Authors: Qi Hui Poh, Alin Rai, Irena I śka Carmichael, Lois A Salamonsen, David W Greening Tags: Research Article Source Type: research

Resourcing, annotating, and analysing synthetic peptides of SARS ‐CoV‐2 for immunopeptidomics and other immunological studies
In this study, we applied tandem mass spectrometry and proteomic techniques to a library of ∼40,000 synthetic peptides, in order to generate a large dataset of SARS‐CoV‐2 derived peptide MS/MS spectra. On this basis, we built an online knowledgebase, termed virusMS (https://virusms.erc.monash.edu/), to document, annotate and analyse these synthetic peptides and their spectral information. VirusMS incorporates a user ‐friendly interface to facilitate searching, browsing and downloading the database content. Detailed annotations of the peptides, including experimental information, peptide modifications, predicted p...
Source: Proteomics - April 14, 2021 Category: Biochemistry Authors: Chen Li, Jerico Revote, Sri H. Ramarathinam, Shan Zou Chung, Nathan P. Croft, Katherine E. Scull, Ziyi Huang, Rochelle Ayala, Asolina Braun, Nicole A. Mifsud, Patricia T. Illing, Pouya Faridi, Anthony W. Purcell Tags: RESEARCH ARTICLE Source Type: research

Proteomics reveals the potential mechanism of Mrps35 controlling Listeria monocytogenes intracellular proliferation in macrophages
This study provided new insights into understanding thatL. monocytogenes infection changed the basic synthesis or metabolism ‐related proteins of host cells. (Source: Proteomics)
Source: Proteomics - April 9, 2021 Category: Biochemistry Authors: Jiangbei Yuan, Zhangfu Li, Fang Li, Zewei Lin, Siyu Yao, Hang Zhou, Wenhu Liu, Haili Yu, Yang Liu, Fang Liu, Fei Li, Haiying Ran, Junying Zhang, Yi Huang, Qihuan Fu, Liting Wang, Jikui Liu Tags: RESEARCH ARTICLE Source Type: research

Resourcing, annotating and analysing synthetic peptides of SARS ‐CoV‐2 for immunopeptidomics and other immunological studies
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - April 8, 2021 Category: Biochemistry Authors: Chen Li, Jerico Revote, Sri H. Ramarathinam, Shan Zou Chung, Nathan P. Croft, Katherine E. Scull, Ziyi Huang, Rochelle Ayala, Asolina Braun, Nicole A. Mifsud, Patricia T. Illing, Pouya Faridi, Anthony W. Purcell Tags: RESEARCH ARTICLE Source Type: research

A novel role for milk fat globule ‐EGF factor 8 protein (MFGE8) in the mediation of mouse sperm‐extracellular vesicle interactions
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - April 1, 2021 Category: Biochemistry Authors: Natalie A. Trigg, Simone J. Stanger, Wei Zhou, David A. Skerrett ‐Byrne, Petra Sipilä, Matthew D. Dun, Andrew L. Eamens, Geoffry N. De Iuliis, Elizabeth G. Bromfield, Shaun D. Roman, Brett Nixon Tags: RESEARCH ARTICLE Source Type: research

Proteomic analysis of tyrosine phosphorylation induced by exogenous expression of oncogenic kinase fusions identified in lung adenocarcinoma
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - March 27, 2021 Category: Biochemistry Authors: Sebastian A. Wagner, Pawel P. Szczesniak, Andrea Voigt, Justus F. Gr äf, Petra Beli Tags: Research Article Source Type: research

Proteomics reveals the potential mechanism of Mrps35 controlling Listeria intracellular proliferation in macrophages
This study provided new insights into understanding thatListeria infection changed the basic synthesis or metabolism ‐related proteins of host cells.This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - March 25, 2021 Category: Biochemistry Authors: Jiangbei Yuan, Zhangfu Li, Fang Li, Zewei Lin, Siyu Yao, Hang Zhou, Wenhu Liu, Haili Yu, Yang Liu, Fang Liu, Fei Li, Haiying Ran, Junying Zhang, Yi Huang, Qihuan Fu, Liting Wang, Jikui Liu Tags: Research Article Source Type: research

Viewpoint: Extracellular vesicles in the transfusion medicine field: the potential of proteomics
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - March 23, 2021 Category: Biochemistry Authors: Lidia Hermida ‐Nogueira, Ángel García Tags: Viewpoint Source Type: research

Front Cover
Cover Image © Wiley‐VCH GmbH. The image is part of a figure in the article DOI:10.1002/pmic.201900203by Lei Li, Yong Jiang et al. (Source: Proteomics)
Source: Proteomics - March 20, 2021 Category: Biochemistry Tags: Front Cover Source Type: research

Contents: Proteomics 6'21
(Source: Proteomics)
Source: Proteomics - March 20, 2021 Category: Biochemistry Tags: CONTENTS Source Type: research

Editorial Board: Proteomics 6'21
(Source: Proteomics)
Source: Proteomics - March 20, 2021 Category: Biochemistry Tags: EDITORIAL BOARD Source Type: research

Front Cover
Cover Image © Wiley‐VCH GmbH. The image is part of a figure in the article DOI:10.1002/pmic.201900203by Lei Li, Yong Jiang et al. (Source: Proteomics)
Source: Proteomics - March 20, 2021 Category: Biochemistry Tags: Front Cover Source Type: research

Contents: Proteomics 6'21
(Source: Proteomics)
Source: Proteomics - March 20, 2021 Category: Biochemistry Tags: CONTENTS Source Type: research

Editorial Board: Proteomics 6'21
(Source: Proteomics)
Source: Proteomics - March 20, 2021 Category: Biochemistry Tags: EDITORIAL BOARD Source Type: research

Impact of sample containers on gas chromatography mass spectrometry based plasma untargeted and targeted metabolomics
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - March 19, 2021 Category: Biochemistry Authors: Minqi Chen, Zhongqiu Liu, Lingzhi Gong Tags: Research Article Source Type: research

Combining label ‐free and label‐based accurate quantifications with SWATH‐MS: comparison with SRM and PRM for the evaluation of bovine muscle type effects
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - March 18, 2021 Category: Biochemistry Authors: Joanna Bons, Gauthier Husson, Marie Chion, Muriel Bonnet, Myriam Maumy ‐Bertrand, François Delalande, Sarah Cianférani, Frédéric Bertrand, Brigitte Picard, Christine Carapito Tags: RESEARCH ARTICLE Source Type: research

Mouse model of Alzheimer's disease demonstrates differential effects of early disease pathology on various brain regions
AbstractDifferent parts of the brain are affected distinctively in various stages of the Alzheimer's disease (AD) pathogenesis. Identifying the biochemical changes in specific brain regions is key to comprehend the neuropathological mechanisms in early pre ‐symptomatic phases of AD. Quantitative proteomics profiling of four distinct areas of the brain of young APP/PS1 mouse model of AD was performed followed by biochemical pathway enrichment analysis. Findings revealed fundamental compositional and functional shifts even in the early stages of the d isease. This novel study highlights unique proteome and biochemical path...
Source: Proteomics - March 9, 2021 Category: Biochemistry Authors: Liting Deng, Vivek K. Gupta, Yunqi Wu, Kanishka Pushpitha, Nitin Chitranshi, Veer B. Gupta, Matthew J. Fitzhenry, Masoud Zabet Moghaddam, Tim Karl, Ghasem Hosseini Salekdeh, Stuart L. Graham, Paul A. Haynes, Mehdi Mirzaei Tags: Dataset Brief Source Type: research

Front Cover
Cover Image © Wiley‐VCH GmbH. The image is part of a figure in the article DOI:10.1002/pmic.201900203by Lei Li, Yong Jiang et al. (Source: Proteomics)
Source: Proteomics - March 9, 2021 Category: Biochemistry Tags: Front Cover Source Type: research

Contents: Proteomics 5'21
(Source: Proteomics)
Source: Proteomics - March 9, 2021 Category: Biochemistry Tags: CONTENTS Source Type: research

RNF4 —A Paradigm for SUMOylation‐Mediated Ubiquitination
(Source: Proteomics)
Source: Proteomics - March 9, 2021 Category: Biochemistry Tags: CORRECTION Source Type: research

Editorial Board: Proteomics 5'21
(Source: Proteomics)
Source: Proteomics - March 9, 2021 Category: Biochemistry Tags: EDITORIAL BOARD Source Type: research

Front Cover
Cover Image © Wiley‐VCH GmbH. The image is part of a figure in the article DOI:10.1002/pmic.201900203by Lei Li, Yong Jiang et al. (Source: Proteomics)
Source: Proteomics - March 9, 2021 Category: Biochemistry Tags: Front Cover Source Type: research

Contents: Proteomics 5'21
(Source: Proteomics)
Source: Proteomics - March 9, 2021 Category: Biochemistry Tags: CONTENTS Source Type: research

RNF4 —A Paradigm for SUMOylation‐Mediated Ubiquitination
(Source: Proteomics)
Source: Proteomics - March 9, 2021 Category: Biochemistry Tags: CORRECTION Source Type: research

Editorial Board: Proteomics 5'21
(Source: Proteomics)
Source: Proteomics - March 9, 2021 Category: Biochemistry Tags: EDITORIAL BOARD Source Type: research

In ‐depth proteome of perilymph in guinea pig model
In this study, we analyzed samples of perilymph collected from 12 guinea pigs to overcome limited experimental information regarding its proteome. We identified a total of 1413 proteins, establishing a greatly expanded proteome of the previously inferred guinea pig perilymph. This provides a comprehensive proteomic resource for the research community, which will facilitate future molecular ‐phenotypic studies using the guinea pig as an experimental model of relevance to human inner ear biology. (Source: Proteomics)
Source: Proteomics - March 9, 2021 Category: Biochemistry Authors: Jung Hun Lee, Yu ‐Jung Hwang, Hui Li, Hyeyoon Kim, Myung‐Whan Suh, Dohyun Han, Seung‐Ha Oh Tags: DATASET BRIEF Source Type: research

High ‐throughput, in‐depth and estimated absolute quantification of plasma proteome using data‐independent acquisition/mass spectrometry (“HIAP‐DIA”)
AbstractMass spectrometry ‐based plasma proteomics has been demonstrated to be a useful tool capable of quantifying hundreds of proteins in a single LC‐MS/MS experiment, for biomarker discovery or elucidation of disease mechanisms. We developed a novel data‐independent acquisition (DIA)/MS‐based workflow for high‐t hroughput, in‐depth and estimated absolute quantification of plasma proteins (termed HIAP‐DIA), without depleting high‐abundant proteins, in a single‐shot experiment. In HIAP‐DIA workflow, we generated an ultra‐deep cumulative undepleted and depleted spectral library which contained 55,1 57...
Source: Proteomics - March 9, 2021 Category: Biochemistry Authors: Yue Zhou, Zengqi Tan, Peng Xue, Yi Wang, Xiang Li, Feng Guan Tags: RESEARCH ARTICLE Source Type: research

Regulation of the microsomal proteome by salicylic acid and  deficiency of phosphatidylinositol‐4‐kinases β1 and β2 in Arabidopsis thaliana
AbstractPhosphatidylinositol ‐4‐kinases β1 and β2 (PI4Kβ1/PI4Kβ2), which are responsible for phosphorylation of phosphatidylinositol to phosphatidylinositol‐4‐phosphate, have important roles in plant vesicular trafficking. Moreover, PI4Kβ1/PI4Kβ2 negatively regulates biosynthesis of phytohormone salicylic acid (SA ), a key player in plant immune responses. The study focused on the effect of PI4Kβ1/PI4Kβ2 deficiency and SA level on the proteome of microsomal fraction. For that purpose we used fourArabidopsis thaliana genotypes: wild type; double mutant with impaired function o...
Source: Proteomics - March 9, 2021 Category: Biochemistry Authors: Petra Junkov á, Michaela Neubergerová, Tetiana Kalachova, Olga Valentová, Martin Janda Tags: DATASET BRIEF Source Type: research

First comprehensive proteomics analysis of lysine crotonylation in leaves of peanut (Arachis hypogaea L.)
AbstractLysine crotonylation is an important post ‐translational modification process. Most research in this area has been carried out on mammals and yeast, but there has been little research on it in plants. In the current study, large‐scale lysine crotonylome analysis was performed by a combination of affinity enrichment and high‐resolution LC‐MS/MS analysis. Altogether, 6051 lysine crotonylation sites were identified in 2508 protein groups. Bioinformatics analysis showed that lysine‐crotonylated proteins were involved in many biological processes, such as carbon fixation in photosynthetic organisms, biosynthes...
Source: Proteomics - March 9, 2021 Category: Biochemistry Authors: Manlin Xu, Jianda Luo, Ying Li, Lili Shen, Xia Zhang, Jing Yu, Zhiqing Guo, Juxiang Wu, Yucheng Chi, Jinguang Yang Tags: RESEARCH ARTICLE Source Type: research

An innovative standard for LC ‐MS‐based HCP profiling and accurate quantity assessment: Application to batch consistency in viral vaccine samples
In this study, we developed an innovat ive standard dedicated to MS‐based HCP profiling analysis in order to monitor the consistency of viral vaccine intermediate purification samples. This standard, termed the HCP‐PROFILER standard, is composed of a water‐soluble bead (READYBEADS technology) which, after being added into the sampl e, releases unlabeled peptides in controlled amounts. The standard meets three desired criteria: (1) it is composed of multiple peptides, at different concentration levels, allowing construction of a calibration curve covering the dynamic range of HCPs present in the target sample, ensurin...
Source: Proteomics - March 9, 2021 Category: Biochemistry Authors: Mathieu Trauchessec, Anne Marie Hesse, Alexandra Kraut, Yves Berard, Laura Herment, Tanguy Fortin, Christophe Bruley, Myriam Ferro, Catherine Manin Tags: RESEARCH ARTICLE Source Type: research