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Journal Mol. Cell Proteomics

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FYN and ABL regulate the interaction networks of the DCBLD receptor family.

Anna M Schmoker, Jaye L Weinert, Jacob M Markwood, Kathryn S Albretsen, Michelle L Lunde, Marion E Weir, Alicia M Ebert, Karen L Hinkle, Bryan A Ballif,

The Discoidin, CUB, and LCCL domain-containing protein (DCBLD) family consists of two type-I transmembrane scaffolding receptors, DCBLD1 and DCBLD2, which play important roles in development and cancer. The non-receptor tyrosine kinases FYN and ABL are known to drive phosphorylation of tyrosine residues in YXXP motifs within the intracellular domains of ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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Data, reagents, assays and merits of proteomics for SARS-CoV-2 research and testing.

Jana Zecha, Chien-Yun Lee, Florian P Bayer, Chen Meng, Vincent Grass, Johannes Zerweck, Karsten Schnatbaum, Thomas Michler, Andreas Pichlmair, Christina Ludwig, Bernhard Kuster,

As the SARS-CoV-2 pandemic continues to spread, thousands of scientists around the globe have changed research direction to understand better how the virus works and to find out how it may be tackled. The number of manuscripts on preprint servers is soaring and peer-reviewed publications using mass spectrometry-based proteomics are ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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Measuring site-specific glycosylation similarity between influenza A virus variants with statistical certainty.

Deborah Chang, William Edwin Hackett, Lei Zhong, Xiu-Feng Wan, Joseph Zaia,

Influenza A virus (IAV) mutates rapidly, resulting in antigenic drift and poor year-to-year vaccine effectiveness. One challenge in designing effective vaccines is that genetic mutations frequently cause amino acid variations in IAV envelope protein hemagglutinin (HA) that create new N-glycosylation sequons; resulting N-glycans cause antigenic shielding, allowing viral escape from ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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Accurate MS-based Rab10 phosphorylation stoichiometry determination as readout for LRRK2 activity in Parkinson's disease.

Ozge Karayel, Francesca Tonelli, Sebastian Virreira Winter, Philipp Emanuel Geyer, Ying Fan, Esther M Sammler, Dario Alessi, Martin Steger, Matthias Mann,

Pathogenic mutations in the Leucine-rich repeat kinase 2 (LRRK2) are the predominant genetic cause of Parkinson's disease (PD). They increase its activity, resulting in augmented Rab10-Thr73 phosphorylation and conversely, LRRK2 inhibition decreases pRab10 levels. Currently, there is no assay to quantify pRab10 levels for drug target engagement or patient stratification. ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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Proteomics and Metaproteomics Add Functional, Taxonomic and Biomass Dimensions to Modeling the Ecosystem at the Mucosal-Luminal Interface.

Leyuan Li, Daniel Figeys,

Recent efforts in gut microbiome studies have highlighted the importance of explicitly describing the ecological processes beyond correlative analysis. However, we are still at the early stage of understanding the organizational principles of the gut ecosystem, partially due to the limited information provided by currently used analytical tools in ecological ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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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,

Intact glycopeptide identification has long been known as a key and challenging barrier to the comprehensive and accurate understanding the role of glycosylation in an organism. Intact glycopeptide analysis is a blossoming field that has received increasing attention in recent years. Mass spectrometry (MS)-based strategies and relative software tools are ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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Proteomics of Galápagos marine iguanas links function of femoral gland proteins to the immune system.

Frederik Tellkamp, Franziska Lang, Alejandro Ibáñez Ricoma, Lena Abraham, Galo Quezada, Stefan Günther, Mario Looso, Fabian Jannik Tann, Daniela Müller, Franz Cemic, Jürgen Hemberger, Sebastian Steinfartz, Marcus Krüger,

Communication between individuals via molecules, termed chemosignaling, is widespread among animal and plant species. However, we lack knowledge on the specific functions of the substances involved for most systems. The femoral gland is an organ that secretes a waxy substance involved in chemical communication in lizards. While the lipids and ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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Recent Advances in Analytical Approaches for Glycan and Glycopeptide Quantitation.

Daniel G Delafield, Lingjun Li,

Growing implications of glycosylation in physiological occurrences and human disease have prompted intensive focus on revealing glycomic perturbations through absolute and relative quantification. Empowered by seminal methodologies and increasing capacity for detection, identification, and characterization, the past decade has provided a significant increase in the number of suitable strategies for ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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Open database searching enables the identification and comparison of bacterial glycoproteomes without defining glycan compositions prior to searching.

Ameera Raudah Ahmad Izaham, Nichollas E Scott,

Mass spectrometry has become an indispensable tool for the characterisation of glycosylation across biological systems. Our ability to generate rich fragmentation of glycopeptides has dramatically improved over the last decade yet our informatic approaches still lag behind. While glycoproteomic informatics approaches using glycan databases have attracted considerable attention, database independent ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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The insulin receptor adaptor IRS2 is an APC/C substrate that promotes cell cycle protein expression and a robust spindle assembly checkpoint.

Sandhya Manohar, Qing Yu, Steven P Gygi, Randall Wharton King,

Insulin receptor substrate 2 (IRS2) is an essential adaptor that mediates signaling downstream of the insulin receptor and other receptor tyrosine kinases. Transduction through IRS2-dependent pathways is important for coordinating metabolic homeostasis, and dysregulation of IRS2 causes systemic insulin signaling defects. Despite the importance of maintaining proper IRS2 abundance, little ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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An interaction network of RNA-binding proteins involved in Drosophila oogenesis.

Prashali Bansal, Johannes Madlung, Kristina Schaaf, Boris Macek, Fulvia Bono,

During Drosophila oogenesis, the localization and translational regulation of maternal transcripts relies on RNA-binding proteins (RBPs). Many of these RBPs localize several mRNAs and may have additional direct interaction partners to regulate their functions. Using immunoprecipitation from whole Drosophilaovaries coupled to mass spectrometry, we examined protein-protein associations of 6 GFP-tagged ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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Ionizing radiation-induced proteomic oxidation in Escherichia coli.

Steven T Bruckbauer, Benjamin B Minkoff, Deyang Yu, Vincent L Cryns, Michael M Cox, Michael R Sussman,

Recent work has begun to investigate the role of protein damage in cell death due to ionizing radiation (IR) exposure, but none have been performed on a proteome-wide basis, nor have they utilized mass spectrometry (MS) to determine chemical identity of the amino acid side chain alteration. Here, we use ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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Kir2.1 interactome mapping uncovers PKP4 as a modulator of the Kir2.1-regulated inward rectifier potassium currents.

Sung-Soo Park, Daniela Ponce-Balbuena, Rork Kuick, Guadalupe Guerrero-Serna, Justin Yoon, Dattatreya Mellacheruvu, Kevin P Conlon, Venkatesha Basrur, Alexey I Nesvizhskii, José Jalife, Jean-François Rual,

Kir2.1, a strong inward rectifier potassium channel encoded by the KCNJ2 gene, is a key regulator of the resting membrane potential of the cardiomyocyte and plays an important role in controlling ventricular excitation and action potential duration in the human heart. Mutations in KCNJ2 result in inheritable cardiac diseases in ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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Depolarization-dependent induction of site-specific changes in sialylation on N-linked glycoproteins in rat nerve terminals.

Inga Boll, Pia Jensen, Veit Schwämmle, Martin R Larsen,

Synaptic transmission leading to release of neurotransmitters in the nervous system is a fast and highly dynamic process. Previously, protein interaction and phosphorylation have been thought to be the main regulators of synaptic transmission. Here we show that sialylation of N-linked glycosylation is a novel potential modulator of neurotransmitter release ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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The mouse heart mitochondria N terminome provides insights into ClpXP-mediated proteolysis.

Eduard Hofsetz, Fatih Demir, Karolina Szczepanowska, Alexandra Kukat, Jayachandran Kizhakkedathu, Aleksandra Trifunovic, Pitter F Huesgen,

The mammalian mitochondrial proteome consists of more than 1100 annotated proteins and their proteostasis is regulated by only a few ATP-dependent protease complexes. Technical advances in protein mass spectrometry allowed for detailed description of the mitoproteome from different species and tissues and their changes under specific conditions. However, protease-substrate relations ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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Differential complex formation via paralogs in the human Sin3 protein interaction network.

Mark K Adams, Charles A S Banks, Janet L Thornton, Cassandra Kempf, Ying Zhang, Sayem Miah, Yan Hao, Mihaela E Sardiu, Maxime Killer, Gaye Hattem, Alexis Murray, Maria Katt, Laurence A Florens, Michael P Washburn,

Despite the continued analysis of HDAC inhibitors in clinical trials, the heterogeneous nature of the protein complexes they target limits our understanding of the beneficial and off-target effects associated with their application. Among the many HDAC protein complexes found within the cell, Sin3 complexes are conserved from yeast to humans ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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Identification of tumor antigens in the HLA peptidome of patient-derived xenograft tumors in mouse.

Nataly Mancette Rijensky, Netta R Blondheim Shraga, Eilon Barnea, Nir Peled, Eli Rosenbaum, Aron Popovtzer, Solomon M Stemmer, Alejandro Livoff, Mark Shlapobersky, Neta Moskovits, Dafna Perry, Eitan Rubin, Itzhak Haviv, Arie Admon,

Personalized cancer immunotherapy targeting patient-specific cancer/testis antigens (CTA) and neoantigens may benefit from large-scale tumor human leukocyte antigen (HLA) peptidome (immunopeptidome) analysis, which aims to accurately identify antigens presented by tumor cells. While significant efforts have been invested in analyzing the HLA peptidomes of fresh tumors, it is often impossible ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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The Aspergillus fumigatus secretome alters the proteome of Pseudomonas aeruginosa to stimulate bacterial growth: implications for co-infection .

Anatte Margalit, James C Carolan, David Shehan, Kevin Kavanagh,

Individuals with cystic fibrosis are susceptible to co-infection by Aspergillus fumigatus and Pseudomonas aeruginosa. Despite the persistence of A.  fumigatus in the cystic fibrosis lung P. aeruginosa eventually predominates as the primary pathogen. Several factors are likely to facilitate P. aeruginosa colonization in the airways, including alterations to the microbial ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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PolySTest: Robust statistical testing of proteomics data with missing values improves detection of biologically relevant features.

Veit Schwämmle, Christina E Hagensen, Adelina Rogowska-Wrzesinska, Ole N Jensen,

Statistical testing remains one of the main challenges for high-confidence detection of differentially regulated proteins or peptides in large-scale quantitative proteomics experiments by mass spectrometry. Statistical tests need to be sufficiently robust to deal with experiment intrinsic data structures and variations and often also reduced feature coverage across different biological ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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Changes in the oligodendrocyte progenitor cell proteome with ageing.

Alerie G de la Fuente, Rayner M L Queiroz, Tanay Ghosh, Christopher E McMurran, Juan F Cubillos, Dwight E Bergles, Denise C Fitzgerald, Clare A Jones, Kathryn S Lilley, Colin P Glover, Robin J M Franklin,

Following central nervous system (CNS) demyelination, adult oligodendrocyte progenitor cells (OPCs) can differentiate into new myelin-forming oligodendrocytes in a regenerative process called remyelination. While remyelination is very efficient in young adults, its efficiency declines progressively with ageing. Here we performed proteomic analysis of OPCs freshly isolated from the brains of ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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Dynamic transcriptomic and phosphoproteomic analysis during cell wall stress in Aspergillus nidulans.

Cynthia Chelius, Walker Huso, Samantha Reese, Alex Doan, Stephen Lincoln, Kelsi Lawson, Bao Tran, Raj Purohit, Trevor Glaros, Ranjan Srivastava, Steven Harris, Mark R Marten,

The fungal cell-wall integrity signaling (CWIS) pathway regulates cellular response to environmental stress to enable wall repair and resumption of normal growth.  This complex, interconnected, pathway has been only partially characterized in filamentous fungi.  To better understand the dynamic cellular response to wall perturbation, a β-glucan synthase inhibitor (micafungin) was ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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Identification of lysine acetylation sites on MERS-CoV replicase pp1ab.

Lin Zhu, Sin-Yee Fung, Guangshan Xie, Lok-Yin Roy Wong, Dong Yan Jin, Zongwei Cai,

MERS is a life-threatening disease and MERS-CoV has the potential to cause the next pandemic. Protein acetylation is known to play a crucial role in host response to viral infection. Acetylation of viral proteins encoded by other RNA viruses have been reported to affect viral replication. It is therefore of ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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Opening ASBMB publications freely to all.

Lila M Gierasch, Nicholas O Davidson, Kerry-Anne Rye, Alma L Burlingame,

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, 19(6):914-915]

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Perlecan Knockdown Significantly Alters Extracellular Matrix Composition and Organization During Cartilage Development.

Alexander R Ocken, Madeline M Ku, Tamara L Kinzer-Ursem, Sarah Calve,

Perlecan is a critical proteoglycan found in the extracellular matrix (ECM) of cartilage. In healthy cartilage, perlecan regulates cartilage biomechanics and we previously demonstrated perlecan deficiency leads to reduced cellular and ECM stiffness in vivo This change in mechanics may lead to the early onset osteoarthritis seen in disorders resulting ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, 19(7):1220-1235]

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Proteomics of Campylobacter jejuni growth in deoxycholate reveals Cj0025c as a cystine transport protein required for wild-type human infection phenotypes.

Lok Man, Ashleigh L Dale, William P Klare, Joel A Cain, Zeynep Sumer-Bayraktar, Paula Niewold, Nestor Solis, Stuart J Cordwell,

Campylobacter jejuni is a major cause of food-borne gastroenteritis. Proteomics by label-based two-dimensional liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) identified proteins associated with growth in 0.1% sodium deoxycholate (DOC, a component of gut bile salts), and system-wide validation was performed by data-independent acquisition (DIA-SWATH-MS). LC-MS/MS quantified 1326 proteins ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2020, :]

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