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Interactome analysis identifies the role of BZW2 in promoting endoplasmic reticulum-mitochondrial contact and mitochondrial metabolism
Mol Cell Proteomics. 2023 Dec 26:100709. doi: 10.1016/j.mcpro.2023.100709. Online ahead of print.ABSTRACTUnderstanding the molecular functions of less-studied proteins is an important task of life science research. Despite reports of BZW2 (Basic leucine zipper and W2 domain-containing protein 2) promoting cancer progression first emerging in 2017, little is known about its molecular function. Using a quantitative proteomic approach to identify its interacting proteins, we found that BZW2 interacts with both endoplasmic reticulum (ER) and mitochondrial proteins. We thus hypothesized that BZW2 localizes to and promotes the f...
Source: Molecular and Cellular Proteomics : MCP - December 28, 2023 Category: Molecular Biology Authors: George Maio Mike Smith Ruchika Bhawal Sheng Zhang Jeremy M Baskin Jenny Li Hening Lin Source Type: research

Deep learning prediction boosts phosphoproteomics-based discoveries through improved phosphopeptide identification
Mol Cell Proteomics. 2023 Dec 26:100707. doi: 10.1016/j.mcpro.2023.100707. Online ahead of print.ABSTRACTShotgun phosphoproteomics enables high-throughput analysis of phosphopeptides in biological samples. One of the primary challenges associated with this technology is the relatively low rate of phosphopeptide identification during data analysis. This limitation hampers the full realization of the potential offered by shotgun phosphoproteomics. Here we present DeepRescore2, a computational workflow that leverages deep learning-based retention time and fragment ion intensity predictions to improve phosphopeptide identifica...
Source: Molecular and Cellular Proteomics : MCP - December 28, 2023 Category: Molecular Biology Authors: Xinpei Yi Bo Wen Shuyi Ji Alex Saltzman Eric J Jaehnig Jonathan T Lei Qiang Gao Bing Zhang Source Type: research

msqrob2PTM: differential abundance and differential usage analysis of MS-based proteomics data at the post-translational modification and peptidoform level
Mol Cell Proteomics. 2023 Dec 26:100708. doi: 10.1016/j.mcpro.2023.100708. Online ahead of print.ABSTRACTIn the era of open-modification search engines, more post-translational modifications than ever can be detected by LC-MS/MS-based proteomics. This development can switch proteomics research into a higher gear, as PTMs are key in many cellular pathways important in cell proliferation, migration, metastasis and ageing. However, despite these advances in modification identification, statistical methods for PTM-level quantification and differential analysis have yet to catch up. This absence can partly be explained by stati...
Source: Molecular and Cellular Proteomics : MCP - December 28, 2023 Category: Molecular Biology Authors: Nina Demeulemeester Marie G ébelin Lucas Caldi Gomes Paul Lingor Christine Carapito Lennart Martens Lieven Clement Source Type: research

Multiplexed Antibody Glycosylation Profiling Using Dual Enzyme Digestion and Liquid Chromatography-Triple Quadrupole Mass Spectrometry Method
In this study, we have developed an analytical workflow using antibody-light-chain affinity beads to purify IgG, IgA, and IgM from 16 μL of human plasma. Dual enzymes, trypsin and Glu-C, were used during on-bead digestion to obtain enzymatic glycopeptides and protein-specific surrogate peptides. Ultra-high-performance liquid chromatography coupled with triple quadrupole mass spectrometry was used in order to determine the sensitivity and specificity. Our platform targets 95 glycopeptides across the IgG, IgA, and IgM isotypes, as well as eight surrogate peptides representing total IgG, four IgG classes, two IgA classes, an...
Source: Molecular and Cellular Proteomics : MCP - December 28, 2023 Category: Molecular Biology Authors: Yu-Hsuan Cheng Chih-Hsin Lee San-Yuan Wang Chia-Yi Chou Yun-Jung Yang Chih-Chin Kao Hsin-Yi Wu Yushi Dong Wen-Ying Hung Ching-Yi Su Shih-Ting Tseng I-Lin Tsai Source Type: research

Interactome analysis identifies the role of BZW2 in promoting endoplasmic reticulum-mitochondrial contact and mitochondrial metabolism
Mol Cell Proteomics. 2023 Dec 26:100709. doi: 10.1016/j.mcpro.2023.100709. Online ahead of print.ABSTRACTUnderstanding the molecular functions of less-studied proteins is an important task of life science research. Despite reports of BZW2 (Basic leucine zipper and W2 domain-containing protein 2) promoting cancer progression first emerging in 2017, little is known about its molecular function. Using a quantitative proteomic approach to identify its interacting proteins, we found that BZW2 interacts with both endoplasmic reticulum (ER) and mitochondrial proteins. We thus hypothesized that BZW2 localizes to and promotes the f...
Source: Molecular and Cellular Proteomics : MCP - December 28, 2023 Category: Molecular Biology Authors: George Maio Mike Smith Ruchika Bhawal Sheng Zhang Jeremy M Baskin Jenny Li Hening Lin Source Type: research

Deep learning prediction boosts phosphoproteomics-based discoveries through improved phosphopeptide identification
Mol Cell Proteomics. 2023 Dec 26:100707. doi: 10.1016/j.mcpro.2023.100707. Online ahead of print.ABSTRACTShotgun phosphoproteomics enables high-throughput analysis of phosphopeptides in biological samples. One of the primary challenges associated with this technology is the relatively low rate of phosphopeptide identification during data analysis. This limitation hampers the full realization of the potential offered by shotgun phosphoproteomics. Here we present DeepRescore2, a computational workflow that leverages deep learning-based retention time and fragment ion intensity predictions to improve phosphopeptide identifica...
Source: Molecular and Cellular Proteomics : MCP - December 28, 2023 Category: Molecular Biology Authors: Xinpei Yi Bo Wen Shuyi Ji Alex Saltzman Eric J Jaehnig Jonathan T Lei Qiang Gao Bing Zhang Source Type: research

msqrob2PTM: differential abundance and differential usage analysis of MS-based proteomics data at the post-translational modification and peptidoform level
Mol Cell Proteomics. 2023 Dec 26:100708. doi: 10.1016/j.mcpro.2023.100708. Online ahead of print.ABSTRACTIn the era of open-modification search engines, more post-translational modifications than ever can be detected by LC-MS/MS-based proteomics. This development can switch proteomics research into a higher gear, as PTMs are key in many cellular pathways important in cell proliferation, migration, metastasis and ageing. However, despite these advances in modification identification, statistical methods for PTM-level quantification and differential analysis have yet to catch up. This absence can partly be explained by stati...
Source: Molecular and Cellular Proteomics : MCP - December 28, 2023 Category: Molecular Biology Authors: Nina Demeulemeester Marie G ébelin Lucas Caldi Gomes Paul Lingor Christine Carapito Lennart Martens Lieven Clement Source Type: research

Multiplexed Antibody Glycosylation Profiling Using Dual Enzyme Digestion and Liquid Chromatography-Triple Quadrupole Mass Spectrometry Method
In this study, we have developed an analytical workflow using antibody-light-chain affinity beads to purify IgG, IgA, and IgM from 16 μL of human plasma. Dual enzymes, trypsin and Glu-C, were used during on-bead digestion to obtain enzymatic glycopeptides and protein-specific surrogate peptides. Ultra-high-performance liquid chromatography coupled with triple quadrupole mass spectrometry was used in order to determine the sensitivity and specificity. Our platform targets 95 glycopeptides across the IgG, IgA, and IgM isotypes, as well as eight surrogate peptides representing total IgG, four IgG classes, two IgA classes, an...
Source: Molecular and Cellular Proteomics : MCP - December 28, 2023 Category: Molecular Biology Authors: Yu-Hsuan Cheng Chih-Hsin Lee San-Yuan Wang Chia-Yi Chou Yun-Jung Yang Chih-Chin Kao Hsin-Yi Wu Yushi Dong Wen-Ying Hung Ching-Yi Su Shih-Ting Tseng I-Lin Tsai Source Type: research

Interactome analysis identifies the role of BZW2 in promoting endoplasmic reticulum-mitochondrial contact and mitochondrial metabolism
Mol Cell Proteomics. 2023 Dec 26:100709. doi: 10.1016/j.mcpro.2023.100709. Online ahead of print.ABSTRACTUnderstanding the molecular functions of less-studied proteins is an important task of life science research. Despite reports of BZW2 (Basic leucine zipper and W2 domain-containing protein 2) promoting cancer progression first emerging in 2017, little is known about its molecular function. Using a quantitative proteomic approach to identify its interacting proteins, we found that BZW2 interacts with both endoplasmic reticulum (ER) and mitochondrial proteins. We thus hypothesized that BZW2 localizes to and promotes the f...
Source: Molecular and Cellular Proteomics : MCP - December 28, 2023 Category: Molecular Biology Authors: George Maio Mike Smith Ruchika Bhawal Sheng Zhang Jeremy M Baskin Jenny Li Hening Lin Source Type: research

Deep learning prediction boosts phosphoproteomics-based discoveries through improved phosphopeptide identification
Mol Cell Proteomics. 2023 Dec 26:100707. doi: 10.1016/j.mcpro.2023.100707. Online ahead of print.ABSTRACTShotgun phosphoproteomics enables high-throughput analysis of phosphopeptides in biological samples. One of the primary challenges associated with this technology is the relatively low rate of phosphopeptide identification during data analysis. This limitation hampers the full realization of the potential offered by shotgun phosphoproteomics. Here we present DeepRescore2, a computational workflow that leverages deep learning-based retention time and fragment ion intensity predictions to improve phosphopeptide identifica...
Source: Molecular and Cellular Proteomics : MCP - December 28, 2023 Category: Molecular Biology Authors: Xinpei Yi Bo Wen Shuyi Ji Alex Saltzman Eric J Jaehnig Jonathan T Lei Qiang Gao Bing Zhang Source Type: research

Remodelling of the cardiac extracellular matrix proteome during chronological and pathological ageing
Mol Cell Proteomics. 2023 Dec 21:100706. doi: 10.1016/j.mcpro.2023.100706. Online ahead of print.ABSTRACTImpaired extracellular matrix (ECM) remodelling is a hallmark of many chronic inflammatory disorders that can lead to cellular dysfunction, ageing, and disease progression. The ECM of the aged heart and its effects on cardiac cells during chronological and pathological ageing are poorly understood across species. For this purpose, we first used mass spectrometry-based proteomics to quantitatively characterize age-related remodelling of the left ventricle (LV) of mice and humans during chronological and pathological (Hut...
Source: Molecular and Cellular Proteomics : MCP - December 23, 2023 Category: Molecular Biology Authors: Deolinda Santinha Andreia Vila ça Lu ís Estronca Svenja C Sch üler Catherine Bartoli Annachiara De Sandre-Giovannoli Arnaldo Figueiredo Maximillian Quaas Tilo Pompe Alessandro Ori Lino Ferreira Source Type: research

Remodelling of the cardiac extracellular matrix proteome during chronological and pathological ageing
Mol Cell Proteomics. 2023 Dec 21:100706. doi: 10.1016/j.mcpro.2023.100706. Online ahead of print.ABSTRACTImpaired extracellular matrix (ECM) remodelling is a hallmark of many chronic inflammatory disorders that can lead to cellular dysfunction, ageing, and disease progression. The ECM of the aged heart and its effects on cardiac cells during chronological and pathological ageing are poorly understood across species. For this purpose, we first used mass spectrometry-based proteomics to quantitatively characterize age-related remodelling of the left ventricle (LV) of mice and humans during chronological and pathological (Hut...
Source: Molecular and Cellular Proteomics : MCP - December 23, 2023 Category: Molecular Biology Authors: Deolinda Santinha Andreia Vila ça Lu ís Estronca Svenja C Sch üler Catherine Bartoli Annachiara De Sandre-Giovannoli Arnaldo Figueiredo Maximillian Quaas Tilo Pompe Alessandro Ori Lino Ferreira Source Type: research

Remodelling of the cardiac extracellular matrix proteome during chronological and pathological ageing
Mol Cell Proteomics. 2023 Dec 21:100706. doi: 10.1016/j.mcpro.2023.100706. Online ahead of print.ABSTRACTImpaired extracellular matrix (ECM) remodelling is a hallmark of many chronic inflammatory disorders that can lead to cellular dysfunction, ageing, and disease progression. The ECM of the aged heart and its effects on cardiac cells during chronological and pathological ageing are poorly understood across species. For this purpose, we first used mass spectrometry-based proteomics to quantitatively characterize age-related remodelling of the left ventricle (LV) of mice and humans during chronological and pathological (Hut...
Source: Molecular and Cellular Proteomics : MCP - December 23, 2023 Category: Molecular Biology Authors: Deolinda Santinha Andreia Vila ça Lu ís Estronca Svenja C Sch üler Catherine Bartoli Annachiara De Sandre-Giovannoli Arnaldo Figueiredo Maximillian Quaas Tilo Pompe Alessandro Ori Lino Ferreira Source Type: research

Remodelling of the cardiac extracellular matrix proteome during chronological and pathological ageing
Mol Cell Proteomics. 2023 Dec 21:100706. doi: 10.1016/j.mcpro.2023.100706. Online ahead of print.ABSTRACTImpaired extracellular matrix (ECM) remodelling is a hallmark of many chronic inflammatory disorders that can lead to cellular dysfunction, ageing, and disease progression. The ECM of the aged heart and its effects on cardiac cells during chronological and pathological ageing are poorly understood across species. For this purpose, we first used mass spectrometry-based proteomics to quantitatively characterize age-related remodelling of the left ventricle (LV) of mice and humans during chronological and pathological (Hut...
Source: Molecular and Cellular Proteomics : MCP - December 23, 2023 Category: Molecular Biology Authors: Deolinda Santinha Andreia Vila ça Lu ís Estronca Svenja C Sch üler Catherine Bartoli Annachiara De Sandre-Giovannoli Arnaldo Figueiredo Maximillian Quaas Tilo Pompe Alessandro Ori Lino Ferreira Source Type: research

Phosphorylation dynamics in a flg22-induced, G-protein dependent network reveals the RGS1 phosphatase
Mol Cell Proteomics. 2023 Dec 20:100705. doi: 10.1016/j.mcpro.2023.100705. Online ahead of print.ABSTRACTThe Microbe Associated Molecular Pattern flg22 is recognized in a FLAGELLIN-SENSITVE 2-dependent manner in root tip cells. Here, we show a rapid and massive change in protein abundance and phosphorylation state of the Arabidopsis root cell proteome in wildtype and a mutant deficient in heterotrimeric G-protein-coupled signaling. flg22-induced changes fall on proteins comprising a subset of this proteome, the heterotrimeric G protein interactome, and on highly populated hubs of the immunity network. Approximately 95% of ...
Source: Molecular and Cellular Proteomics : MCP - December 22, 2023 Category: Molecular Biology Authors: Justin M Watkins Christian Montes Natalie M Clark Gaoyuan Song Celio Cabral Oliveira Bharat Mishra Libuse Brachova Clara M Seifert Malek S Mitchell Jing Yang Pedro Augusto Braga Dos Reis Daisuke Urano M Shahid Muktar Justin W Walley Alan M Jones Source Type: research