Proteomic Analysis of the Lake Trout (Salvelinus namaycush) Heart and Blood: the beginning of a comprehensive lake trout protein database
This study builds on our previous work by continuing to build the first comprehensive lake trout protein database and provides insight into protein homology through evolutionary relationships. This data is available via the PRIDE partner repository with the dataset identifier  PXD023970.This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - October 22, 2021 Category: Biochemistry Authors: Emmalyn J. Dupree, Zaen Manzoor, Shelby Alwine, Bernard S. Crimmins, Thomas M. Holsen, Costel C. Darie Tags: DATASET BRIEF Source Type: research

Proteomic and electron microscopy study of myogenic differentiation of alveolar mucosa multipotent mesenchymal stromal cells in 3D culture
AbstractMyocyte differentiation is featured by adaptation processes, including mitochondria repopulation and cytoskeleton re-organization. The difference between monolayer and spheroid cultured cells at the proteomic level is uncertain. We cultivated alveolar mucosa multipotent mesenchymal stromal cells in spheroids in a myogenic way for the proper conditioning of ECM architecture and cell morphology, which induced spontaneous myogenic differentiation of cells within spheroids. Electron microscopy analysis was used for the morphometry of mitochondria biogenesis, and proteomic was used complementary to unveil events underly...
Source: Proteomics - October 21, 2021 Category: Biochemistry Authors: Irina N. Saburina, Nastasia V. Kosheleva, Arthur T. Kopylov, Tatiana V. Lipina, Marina E. Krasina, Irina M. Zurina, Anastasiya A. Gorkun, Svetlana S. Girina, Andrey A. Pulin, Anna L. Kaysheva, Sergey G. Morozov Tags: Research Article Source Type: research

A pre ‐processing pipeline to quantify, visualize and reduce technical variation in protein microarray studies
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - October 21, 2021 Category: Biochemistry Authors: Sophie B érubé, Tamaki Kobayashi, Amy Wesolowski, Douglas E. Norris, Ingo Ruczinski, William J. Moss, Thomas A. Louis Tags: Technical Brief Source Type: research

Passages in culture and stimulation conditions influence protein expression of primary fibroblasts
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - October 20, 2021 Category: Biochemistry Authors: Solange Vivier, Aur élien Chepy, Fabrice Bray, Thomas Guerrier, Silvia Speca, Stéphanie Flament, Manel Jendoubi, Maïté Balden, Christian Rolando, Eric Hachulla, David Launay, Sylvain Dubucquoi, Vincent Sobanski Tags: ACCELERATED ARTICLE Source Type: research

Front Cover
The cover image is based on the Accelerated ArticleCD99 and polymeric immunoglobulin receptor peptides deregulation in critical COVID-19: A potential link to molecular pathophysiology? by Justyna Siwy et al.,10.1002/pmic.202100133, and the Accelerated ArticleSGLT2-Inhibition reverts urinary peptide changes associated with severe COVID-19: An in-silico proof-of-principle of proteomics-based drug repurposing by Agnieszka Latosinska et al.,10.1002/pmic.202100160. (Source: Proteomics)
Source: Proteomics - October 16, 2021 Category: Biochemistry Tags: FRONT COVER Source Type: research

Contents: Proteomics 20'21
(Source: Proteomics)
Source: Proteomics - October 16, 2021 Category: Biochemistry Tags: CONTENTS Source Type: research

Editorial Board: Proteomics 20'21
(Source: Proteomics)
Source: Proteomics - October 16, 2021 Category: Biochemistry Tags: EDITORIAL BOARD Source Type: research

Secretome analysis of human schwann cells derived from malignant peripheral nerve sheath tumor
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - October 15, 2021 Category: Biochemistry Authors: Aysha Ferdoushi, M. Fairuz B. Jamaluddin, Xiang Li, Jay Pundavela, Sam Faulkner, Hubert Hondermarck Tags: TECHNICAL BRIEF Source Type: research

Nanopore sensing of γ‐cyclodextrin induced host‐guest interaction to reverse the binding of perfluorooctanoic acid to human serum albumin
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - October 14, 2021 Category: Biochemistry Authors: Xiaojun Wei, Qian Wang, Chang Liu Tags: TECHNICAL BRIEF Source Type: research

Progress in methodologies and quality ‐control strategies in protein cross‐linking mass spectrometry
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - October 14, 2021 Category: Biochemistry Authors: Kumar Yugandhar, Qiuye Zhao, Shobhita Gupta, Dapeng Xiong, Haiyuan Yu Tags: REVIEW Source Type: research

Identification of active deubiquitinases in the chicken tissues
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - October 13, 2021 Category: Biochemistry Authors: Bindu Nanduri, Cathy R. Gresham, Gary Jones, Richard H. Bailey, Mariola J Edelmann Tags: DATASET BRIEF Source Type: research

Universal and cross ‐cancer prognostic biomarkers for predicting survival risk of cancer patients from expression profile of apoptotic pathway genes
(Source: Proteomics)
Source: Proteomics - October 13, 2021 Category: Biochemistry Authors: Chakit Arora, Dilraj Kaur, Gajendra P. S. Raghava Tags: Research Article Source Type: research

Insights from tissue “omics” analysis on intestinal remodeling in celiac disease
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - October 11, 2021 Category: Biochemistry Authors: Jorunn Stamnaes Tags: Research Article Source Type: research

Molecular characterization of triple negative breast cancer formaldehyde ‐fixed paraffin‐embedded samples by data‐independent acquisition proteomics
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - October 9, 2021 Category: Biochemistry Authors: Silvia Garc ía‐Adrián, Lucía Trilla‐Fuertes, Angelo Gámez‐Pozo, Cristina Chiva, Rocío López‐Vacas, Elena López‐Camacho, Andrea Zapater‐Moros, María I. Lumbreras‐Herrera, David Hardisson, Laura Yébenes, Pilar Zamora, Eduar Tags: DATASET BRIEF Source Type: research

Characterization of HLA ‐A*33:03 epitopes via immunoprecipitation and LC‐MS/MS
In this study, we aimed to characterize the peptidome that binds to HLA-A*33:03, which is one of the most prevalent HLA-A alleles in the Northeast Asian population, but poorly studied. For this purpose, we analyzed the HLA-A*33:03 monoallelic B cell line using immunoprecipitation of HLA-A and peptide complexes, followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). In this study, we identified 5731 unique peptides that were associated with HLA A*33:03, and experimentally validated the affinity of 40 peptides for HLA-A*33:03 and their stability in HLA A*33:03-peptides complexes. To our knowledge, this study ...
Source: Proteomics - October 7, 2021 Category: Biochemistry Authors: Amir Khan, Ji ‐Yon Shin, Min Kyung So, Jung‐Hyun Na, Sune Justesen, Adnan Ahmad Ansari, Byoung Joon Ko, Sung‐Min Ahn 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.201900203 by Lei Li, Yong Jiang et al. (Source: Proteomics)
Source: Proteomics - October 5, 2021 Category: Biochemistry Tags: FRONT COVER Source Type: research

Contents: Proteomics 19'21
(Source: Proteomics)
Source: Proteomics - October 5, 2021 Category: Biochemistry Tags: CONTENTS Source Type: research

Editorial Board: Proteomics 19'21
(Source: Proteomics)
Source: Proteomics - October 5, 2021 Category: Biochemistry Tags: EDITORIAL BOARD Source Type: research

Standard abbreviations
(Source: Proteomics)
Source: Proteomics - October 5, 2021 Category: Biochemistry Tags: STANDARD ABBREVIATIONS Source Type: research

Nutrient ‐specific Proteomic Analysis of the Mucin Degrading Bacterium Akkermansia muciniphila
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - October 1, 2021 Category: Biochemistry Authors: Ji ‐Young Lee, Hyeon‐Su Jin, Kyoung Su Kim, Je‐Hyun Baek, Bong‐Soo Kim, Dong‐Woo Lee Tags: DATASET BRIEF Source Type: research

Targeted liquid chromatography ‐tandem mass spectrometry analysis of proteins: Basic principles, applications, and perspectives
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - October 1, 2021 Category: Biochemistry Authors: Arman Kulyyassov, Margaux Fresnais, R émi Longuespée Tags: Research Article Source Type: research

Teaching an old dog new tricks: a lipid membrane ‐based electric immunosensor for real‐time probing of the spike S1 protein subunit from SARS‐CoV‐2
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - September 30, 2021 Category: Biochemistry Authors: Alina Asandei, Loredana Mereuta, Irina Schiopu, Yoonkyung Park, Tudor Luchian Tags: Research Article Source Type: research

Automation of single ‐cell proteomic sample preparation
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - September 28, 2021 Category: Biochemistry Authors: Michal Alexovi č, Ján Sabo, Rémi Longuespée Tags: REVIEW Source Type: research

prPred ‐DRLF: plant R protein predictor using deep representation learning features
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - September 27, 2021 Category: Biochemistry Authors: Yansu Wang, Lei Xu, Quan Zou, Chen Lin Tags: RESEARCH ARTICLE Source Type: research

Proteomics analysis reveals the correlation of programmed ROS ‐autophagy loop and dysregulated G1/S checkpoint with imatinib resistance in Chronic Myeloid Leukemia cells
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - September 26, 2021 Category: Biochemistry Authors: Xiucai Xu, Shihong Yin, Yingli Ren, Chaojie Hu, Aimei Zhang, Ya Lin Tags: Research Article Source Type: research

Characterization of HLA ‐A33:03 epitopes via immunoprecipitation and LC‐MS/MS
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - September 26, 2021 Category: Biochemistry Authors: Amir Khan, JiYon Shin, Min Kyung So, Jung ‐Hyun Na, Sune Justesen, Adnan Ahmad Ansari, Byoung Joon Ko, SungMin Ahn Tags: Dataset Brief Source Type: research

Proteomic analysis of Giardia lamblia and Trichomonas vaginalis flagella reveal unique post ‐translational modifications in tubulin that provide clues to regulation of their motilities
In this study, we have analyzed the tubulin post-translational modification in the protozoan parasitesGiardia lamblia andTrichomonas vaginalis using global, untargeted mass spectrometry. We show that tubulin monoglycylation is a modification localized to the flagella present inG. lamblia but absent inT. vaginalis. We also show the presence of glutamylated tubulin in bothG. lamblia andT. vaginalis. Using MS/MS, we were also able to identify the previously unknown sites of monoglycylation in β-tubulin at E438 and E439 inG. lamblia. Using isolated flagella, we also characterized the flagellar proteome inG. lamblia andT. ...
Source: Proteomics - September 24, 2021 Category: Biochemistry Authors: Aparna Sudhakar, Sathisha Kamanna, Mallikarjun Bojja, Utpal Tatu Tags: RESEARCH ARTICLE Source Type: research

Enhanced identification of tau acetylation and phosphorylation with an engineered aerolysin nanopore
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - September 21, 2021 Category: Biochemistry Authors: Ming ‐Zhu Huo, Zheng‐Li Hu, Yi‐Lun Ying, Yi‐Tao Long Tags: Accelerated Article Source Type: research

Identification of multiple proteins whose interaction with mannitol dehydrogenase is induced by salicylic acid: Implications for unconventional secretion
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - September 13, 2021 Category: Biochemistry Authors: Tricia C. Ho, R. Kevin Blackburn, Michael B. Goshe, John D. Williamson Tags: Dataset Brief Source Type: research

Front Cover
Cover Image © Sri Ramarathinam. (Source: Proteomics)
Source: Proteomics - September 12, 2021 Category: Biochemistry Tags: FRONT COVER Source Type: research

Contents: Proteomics 17 –18'21
(Source: Proteomics)
Source: Proteomics - September 12, 2021 Category: Biochemistry Tags: CONTENTS Source Type: research

Editorial Board: Proteomics 17 –18'21
(Source: Proteomics)
Source: Proteomics - September 12, 2021 Category: Biochemistry Tags: EDITORIAL BOARD Source Type: research

Proteomics special issue: Precision immunology and oncology
(Source: Proteomics)
Source: Proteomics - September 12, 2021 Category: Biochemistry Authors: Sri H. Ramarathinam, Anthony W. Purcell Tags: EDITORIAL Source Type: research

Front Cover
Cover Image © Sri Ramarathinam. (Source: Proteomics)
Source: Proteomics - September 12, 2021 Category: Biochemistry Tags: FRONT COVER Source Type: research

Contents: Proteomics 17 –18'21
(Source: Proteomics)
Source: Proteomics - September 12, 2021 Category: Biochemistry Tags: CONTENTS Source Type: research

Editorial Board: Proteomics 17 –18'21
(Source: Proteomics)
Source: Proteomics - September 12, 2021 Category: Biochemistry Tags: EDITORIAL BOARD Source Type: research

Proteomics special issue: Precision immunology and oncology
(Source: Proteomics)
Source: Proteomics - September 12, 2021 Category: Biochemistry Authors: Sri H. Ramarathinam, Anthony W. Purcell Tags: EDITORIAL Source Type: research

CLN6 deficiency causes selective changes in the lysosomal protein composition
AbstractNeuronal ceroid lipofuscinoses (NCLs) collectively account for the highest prevalence of inherited neurodegenerative diseases in childhood. This disease group is classified by the deposition of similar autofluorescence storage material in lysosomes that is accompanied by seizures, blindness and premature mortality in later disease stages. Defects in several genes affecting various proteins lead to NCL, one of them being CLN6, a transmembrane protein resident in the endoplasmic reticulum. Dysfunctionality of CLN6 causes variant late infantile NCL (vLINCL). The function of CLN6 and how its deficiency affects lysosoma...
Source: Proteomics - September 11, 2021 Category: Biochemistry Authors: Andreas Tuermer, Simone Mausbach, Edgar Kaade, Markus Damme, Marc Sylvester, Volkmar Gieselmann, Melanie Thelen Tags: RESEARCH ARTICLE Source Type: research

RapiGest precipitation depends on peptide concentration
AbstractThe mass spectrometry-compatible surfactant RapiGest promotes the enzymatic digestion of proteins by facilitating their unfolding while retaining enzymatic activity. RapiGest consists of a hydrophilic head and a hydrophobic tail, which can be separated by acid hydrolysis. This allows for removal of RapiGest prior to mass spectrometric analysis via precipitation and solid phase extraction. During in-solution digestion experiments with RapiGest, we noticed a high variability in the formation of precipitates after acid hydrolysis, implying that RapiGest precipitation is sample-dependent. We show that RapiGest hydrolys...
Source: Proteomics - September 6, 2021 Category: Biochemistry Authors: Peter R. Mosen, Robert Hardt, Dominic Winter Tags: TECHNICAL BRIEF Source Type: research

Temporal dynamics of protein and post ‐translational modification abundances in Populus leaf across a diurnal period
(Source: Proteomics)
Source: Proteomics - September 5, 2021 Category: Biochemistry Authors: Him K. Shrestha, Manuel I. Villalobos Solis, Sara S. Jawdy, Gerald A. Tuskan, Xiaohan Yang, Paul E. Abraham Tags: Dataset Brief Source Type: research

Quantitative proteomic analysis of the effects of dietary deprivation of methionine and cystine on A549 xenograft and A549 xenograft ‐bearing mouse
This study provides the first insights into changes within the proteome profile and biological processes upon Met and CySS deprivation in a A549 xenograft mouse model.This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - September 5, 2021 Category: Biochemistry Authors: Hao Yang, Haoyang Zheng, Yue Pan, Weiguo Zhang, Mengjing Yang, Huiling Du, Anan Yu, Ping Li, Xiaoyan Chen, Wei Xie, Kaiming Ren, Ying Zhao, Tianjiao Wang, Xiaoyan He, Zhaoli Zhou Tags: Research Article Source Type: research

Structure of prion β‐oligomers as determined by short‐distance crosslinking constraint‐guided discrete molecular dynamics simulations
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - September 5, 2021 Category: Biochemistry Authors: Jason J. Serpa, Konstantin I. Popov, Evgeniy V. Petrotchenko, Nikolay V. Dokholyan, Christoph H. Borchers Tags: Research Article Source Type: research

SGLT2 ‐Inhibition reverts urinary peptide changes associated with severe COVID‐19: An in‐silico proof‐of‐principle of proteomics‐based drug repurposing
This article is protected by copyright. All rights reserved (Source: Proteomics)
Source: Proteomics - September 4, 2021 Category: Biochemistry Authors: Agnieszka Latosinska, Justyna Siwy, David Z. Cherney, Bruce A. Perkins, Harald Mischak, Joachim Beige Tags: Accelerated Article Source Type: research

Single polypeptide detection using a translocon EXP2 nanopore
AbstractDNA sequencing using nanopores has already been achieved and commercialized; the next step in advancing nanopore technology is towards protein sequencing. Although trials have been reported for discriminating the 20 amino acids using biological nanopores and short peptide carriers, it remains challenging. The size compatibility between nanopores and peptides is one of the issues to be addressed. Therefore, exploring biological nanopores that are suitable for peptide sensing is key in achieving amino acid sequence determination. Here, we focus on EXP2, the transmembrane protein of a translocon from malaria parasites...
Source: Proteomics - September 1, 2021 Category: Biochemistry Authors: Mitsuki Miyagi, Sotaro Takiguchi, Kazuaki Hakamada, Masafumi Yohda, Ryuji Kawano Tags: Research Article Source Type: research