Molecular and Cellular Proteomics : MCP This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.

Analysis of the Healthy Platelet Proteome Identifies a New Form of Domain-Specific O-Fucosylation
Mol Cell Proteomics. 2024 Jan 16;23(2):100717. doi: 10.1016/j.mcpro.2024.100717. Online ahead of print.ABSTRACTPlatelet activation induces the secretion of proteins that promote platelet aggregation and inflammation. However, detailed analysis of the released platelet proteome is hampered by platelets' tendency to preactivate during their isolation and a lack of sensitive protocols for low abundance releasate analysis. Here, we detail the most sensitive analysis to date of the platelet releasate proteome with the detection of >1300 proteins. Unbiased scanning for posttranslational modifications within releasate proteins...
Source: Molecular and Cellular Proteomics : MCP - January 18, 2024 Category: Molecular Biology Authors: Callum B Houlahan Yvonne Kong Bede Johnston Michelle Cielesh The Huong Chau Jemma Fenwick Paul R Coleman Huilin Hao Robert S Haltiwanger Morten Thaysen-Andersen Freda H Passam Mark Larance Source Type: research

The differential translation capabilities of the human DHFR2 gene indicates a developmental and tissue specific endogenous protein of low abundance
Mol Cell Proteomics. 2024 Jan 13:100718. doi: 10.1016/j.mcpro.2024.100718. Online ahead of print.ABSTRACTA functional role has been ascribed to the human Dihydrofolate reductase 2 (DHFR2) gene based on the enzymatic activity of recombinant versions of the predicted translated protein. However, the in vivo function is still unclear. The high amino acid sequence identity (92%) between DHFR2 and its parental homologue, DHFR, makes analysis of the endogenous protein challenging. This paper describes a targeted mass spectrometry proteomics approach in several human cell lines and tissue types to identify DHFR2 specific peptides...
Source: Molecular and Cellular Proteomics : MCP - January 15, 2024 Category: Molecular Biology Authors: Niamh Bookey Paola Drago Kit-Yi Leung Linda Hughes Aoife MacCooey Mari Ozaki Michael Henry Sandra C P De Castro Ivan Doykov Wendy E Heywood Kevin Mills Michelle M Murphy Pere Cavall é-Busquets Susan Campbell Denise Burtenshaw Paula Meleady Paul A Chill N Source Type: research

Stabilizing the Proteomes of Acute Myeloid Leukemia Cells: Implications for Cancer Proteomics
Mol Cell Proteomics. 2024 Jan 12;23(2):100716. doi: 10.1016/j.mcpro.2024.100716. Online ahead of print.ABSTRACTPrevious work has shown that inhibition of abundant myeloid azurophil granule-associated serine proteases (ELANE [neutrophil elastase], PRTN3 [protease 3], and CTSG [Cathepsin G]) is required to stabilize some proteins in myeloid cells. We therefore hypothesized that effective inhibition of these proteases may be necessary for quantitative proteomic analysis of samples containing myeloid cells. To test this hypothesis, we thawed viably preserved acute myeloid leukemia cells from cryovials in the presence or the ab...
Source: Molecular and Cellular Proteomics : MCP - January 14, 2024 Category: Molecular Biology Authors: Robert W Sprung Qiang Zhang Michael H Kramer Matthew C Christopher Petra Erdmann-Gilmore Yiling Mi James P Malone Timothy J Ley R Reid Townsend Source Type: research

Nuclear Phosphoproteome Reveals Prolyl Isomerase PIN1 as a Modulator of Oncogene-Induced Senescence
In this study, we analyzed the changes in the nuclear proteome and phosphoproteome of human lung fibroblast IMR90 cells during the progression of OIS induced by oncogenic RASG12V activation. We found that most of the differentially regulated phosphosites during OIS contained prolyl isomerase PIN1 target motifs, suggesting PIN1 is a key regulator of several promyelocytic leukemia nuclear body proteins, specifically regulating several proteins upon oncogenic Ras activation. We showed that PIN1 knockdown promotes cell proliferation, while diminishing the senescence phenotype and hallmarks of senescence, including p21, p16, an...
Source: Molecular and Cellular Proteomics : MCP - January 12, 2024 Category: Molecular Biology Authors: Rodrigo Mohallem Uma K Aryal Source Type: research

Ion Mobility-Based Enrichment-Free N-Terminomics Analysis Reveals Novel Legumain Substrates in Murine Spleen
Mol Cell Proteomics. 2024 Jan 8;23(2):100714. doi: 10.1016/j.mcpro.2024.100714. Online ahead of print.ABSTRACTAberrant levels of the asparaginyl endopeptidase legumain have been linked to inflammation, neurodegeneration, and cancer, yet our understanding of this protease is incomplete. Systematic attempts to identify legumain substrates have been previously confined to in vitro studies, which fail to mirror physiological conditions and obscure biologically relevant cleavage events. Using high-field asymmetric waveform ion mobility spectrometry (FAIMS), we developed a streamlined approach for proteome and N-terminome analys...
Source: Molecular and Cellular Proteomics : MCP - January 10, 2024 Category: Molecular Biology Authors: Alexander R Ziegler Antoine Dufour Nichollas E Scott Laura E Edgington-Mitchell Source Type: research

Full Mass Range ΦSDM Orbitrap Mass Spectrometry for DIA Proteome Analysis
In conclusion, ΦSDM is an alternative signal processing algorithm for processing Orbitrap data that can improve spectral quality and benefit quantitative accuracy in typical proteomics experiments, especially when using short gradients.PMID:38184013 | PMC:PMC10851225 | DOI:10.1016/j.mcpro.2024.100713 (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - January 6, 2024 Category: Molecular Biology Authors: Sophia Steigerwald Ankit Sinha Kyle L Fort Wen-Feng Zeng Lili Niu Christoph Wichmann Arne Kreutzmann Daniel Mourad Konstantin Aizikov Dmitry Grinfeld Alexander Makarov Matthias Mann Florian Meier Source Type: research

Full Mass Range ΦSDM Orbitrap Mass Spectrometry for DIA Proteome Analysis
In conclusion, ΦSDM is an alternative signal processing algorithm for processing Orbitrap data that can improve spectral quality and benefit quantitative accuracy in typical proteomics experiments, especially when using short gradients.PMID:38184013 | DOI:10.1016/j.mcpro.2024.100713 (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - January 6, 2024 Category: Molecular Biology Authors: Sophia Steigerwald Ankit Sinha Kyle L Fort Wen-Feng Zeng Lili Niu Christoph Wichmann Arne Kreutzmann Daniel Mourad Konstantin Aizikov Dmitry Grinfeld Alexander Makarov Matthias Mann Florian Meier Source Type: research

Recognition of highly branched N-glycans of the porcine whipworm by the immune system
Mol Cell Proteomics. 2024 Jan 3:100711. doi: 10.1016/j.mcpro.2024.100711. Online ahead of print.ABSTRACTGlycans are key to host-pathogen interactions, whereby recognition by the host and immunomodulation by the pathogen can be mediated by carbohydrate binding proteins, such as lectins of the innate immune system, and their glycoconjugate ligands. Previous studies have shown that excretory-secretory products of the porcine nematode parasite Trichuris suis exert immunomodulatory effects in a glycan-dependent manner. To better understand the mechanisms of these interactions, we prepared N-glycans from T. suis and both analyze...
Source: Molecular and Cellular Proteomics : MCP - January 5, 2024 Category: Molecular Biology Authors: Barbara Eckmair Chao Gao Akul Y Mehta Zuzanna Dutkiewicz Jorick Vanbeselaere Richard D Cummings Katharina Paschinger Iain B H Wilson Source Type: research

Acquisition and analysis of DIA-based proteomic data: a comprehensive survey in 2023
Mol Cell Proteomics. 2024 Jan 3:100712. doi: 10.1016/j.mcpro.2024.100712. Online ahead of print.ABSTRACTData-independent acquisition (DIA) mass spectrometry (MS) has emerged as a powerful technology for high-throughput, accurate and reproducible quantitative proteomics. This review provides a comprehensive overview of recent advances in both the experimental and computational methods for DIA proteomics, from data acquisition schemes to analysis strategies and software tools. DIA acquisition schemes are categorized based on the design of precursor isolation windows, highlighting wide-window, overlapping-window, narrow-windo...
Source: Molecular and Cellular Proteomics : MCP - January 5, 2024 Category: Molecular Biology Authors: Ronghui Lou Wenqing Shui 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