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Journal Mol. Cell Proteomics

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Global proteome and phosphoproteome characterization of sepsis-induced kidney injury.

Yi-Han Lin, Maryann P Platt, Haiyan Fu, Yuan Gui, Yanlin Wang, Norberto Gonzalez-Juarbe, Dong Zhou, Yanbao Yu,

Sepsis-induced acute kidney injury (S-AKI) is the most common complication in hospitalized and critically ill patients, highlighted by a rapid decline of kidney function occurring a few hours or days after sepsis onset. Systemic inflammation elicited by microbial infections is believed to lead to kidney damage under immunocompromised conditions. However, ... Read more >>

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

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CIITA-transduced glioblastoma cells uncover a rich repertoire of clinically relevant tumor-associated HLA-II antigens.

Greta Forlani, Justine Michaux, HuiSong Pak, Florian Huber, Elodie Lauret Marie Joseph, Elise Ramia, Brian J Stevenson, Michael Linnebacher, Roberto Accolla, Michal Bassani-Sternberg,

CD4+ T cell responses are crucial for inducing and maintaining effective anti-cancer immunity, and the identification of human leukocyte antigen class II (HLA-II) cancer-specific epitopes is key to the development of potent cancer immunotherapies. In many tumor types, and especially in glioblastoma (GBM), HLA-II complexes are hardly ever naturally expressed. ... Read more >>

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

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Quantitative data independent acquisition glycoproteomics of sparkling wine.

Cassandra L Pegg, Toan K Phung, Christopher H Caboche, Suchada Niamsuphap, Marshall Bern, Kate Howell, Benjamin L Schulz,

Sparkling wine is an alcoholic beverage enjoyed around the world. The sensory properties of sparkling wine depend on a complex interplay between the chemical and biochemical components in the final product. Glycoproteins have been linked to positive and negative qualities in sparkling wine, but the glycosylation profiles of sparkling wine ... Read more >>

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

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Integrated glycoproteomics identifies a role of N-glycosylation and galectin-1 on myogenesis and muscle development.

Ronnie Blazev, Christopher Ashwood, Jodie L Abrahams, Long H Chung, Deanne Francis, Pengyi Yang, Kevin I Watt, Hongwei Qian, Gregory A Quaife-Ryan, James E Hudson, Paul Gregorevic, Morten Thaysen-Andersen, Benjamin L Parker,

Many cell surface and secreted proteins are modified by the covalent addition of glycans that play an important role in the development of multicellular organisms. These glycan modifications enable communication between cells and the extracellular matrix via interactions with specific glycan-binding lectins and the regulation of receptor-mediated signaling. Aberrant protein ... Read more >>

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

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Proteome-wide analysis reveals substrates of E3 ligase RNF146 targeted for degradation.

Litong Nie, Chao Wang, Nan Li, Xu Feng, Namsoo Lee, Dan Su, Mengfan Tang, Fan Yao, Junjie Chen,

Specific E3 ligases target tumor suppressors for degradation. Inhibition of such E3 ligases may be an important approach to cancer treatment. RNF146 is a RING domain and PARylation-dependent E3 ligase that functions as an activator of the β-catenin/Wnt and YAP/Hippo pathways by targeting the degradation of several tumor suppressors. Tankyrases ... Read more >>

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

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A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-based Glycoproteomics.

Nicholas M Riley, Carolyn R Bertozzi, Sharon J Pitteri,

Glycosylation is a prevalent, yet heterogeneous modification with a broad range of implications in molecular biology. This heterogeneity precludes enrichment strategies that can be universally beneficial for all glycan classes. Thus, choice of enrichment strategy has profound implications on experimental outcomes. Here we review common enrichment strategies used in modern ... Read more >>

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

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Methods for Enrichment and Assignment of N-Acetylglucosamine Modification Sites.

Jason Maynard, Robert J Chalkley,

O-GlcNAcylation, the addition of a single N-acetylglucosamine residue to serine and threonine residues of cytoplasmic, nuclear, or mitochondrial proteins, is a widespread regulatory post-translational modification. It is involved in response to nutritional status and stress and its dysregulation is associated with diseases ranging from Alzheimer's to diabetes.  While the modification ... Read more >>

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

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A Novel Mechanism For NF-κB Activation Via IκB Aggregation: Implications For Hepatic Mallory-Denk-Body Induced Inflammation.

Yi Liu, Michael J Trnka, Shenheng Guan, Doyoung Kwon, Do-Hyung Kim, Jane-Jane Chen, Peter A Greer, Alma L Burlingame, Maria Almira Correia,

Mallory-Denk-bodies (MDBs) are hepatic protein aggregates associated with inflammation both clinically and in MDB-inducing models. Similar protein aggregation in neurodegenerative diseases also triggers inflammation and NF-kB activation. However, the precise mechanism that links protein aggregation to NF-kB-activation and inflammatory response remains unclear. Herein we find that treating primary hepatocytes with ... Read more >>

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

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Developments in Mass Spectrometry for Glycosaminoglycan Analysis: A Review.

Lauren E Pepi, Patience Sanderson, Morgan Stickney, I Jonathan Amster,

This review covers recent developments in glycosaminoglycan (GAG) analysis via mass spectrometry (MS). GAGs participate in a variety of biological functions, including cellular communication, wound healing, and anticoagulation, and are important targets for structural characterization. GAGs exhibit a diverse range of structural features due to the variety of O- and ... Read more >>

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

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Temporal quantitative proteomics of mGluR-induced protein translation and phosphorylation in neurons.

Charlotte Agh van Gelder, Renske Penning, Tim Veth, Lisa Ae Catsburg, Casper C Hoogenraad, Harold D MacGillavry, Maarten Altelaar,

At neuronal synapses, activation of group I metabotropic glutamate receptors (mGluR1/5) triggers a form of long-term depression (mGluR-LTD) that relies on new protein synthesis and the internalization of AMPA-type glutamate receptors. Dysregulation of these processes has been implicated in the development of mental disorders such as autism spectrum disorders and ... Read more >>

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

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ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis.

Johannes Griss, Guilherme Viteri, Konstantinos Sidiropoulos, Vy Nguyen, Antonio Fabregat, Henning Hermjakob,

Pathway analyses are key methods to analyse 'omics experiments. Nevertheless, integrating data from different 'omics technologies and different species still requires considerable bioinformatics knowledge.  Here we present the novel ReactomeGSA resource for comparative pathway analyses of multi-omics datasets. ReactomeGSA can be used through Reactome's existing web interface and the novel ... Read more >>

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

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Stoichiometry of Nucleotide Binding to Proteasome AAA+ ATPase Hexamer Established by Native Mass Spectrometry.

Yadong Yu, Haichuan Liu, Zanlin Yu, Halina Ewa Witkowska, Yifan Cheng,

AAA+ ATPases constitute a large family of proteins that are involved in a plethora of cellular processes including DNA disassembly, protein degradation and protein complex disassembly. They typically form a hexametric ring-shaped structure with six subunits in a (pseudo) six-fold symmetry. In a subset of AAA+ ATPases that facilitate protein ... Read more >>

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

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Calculating glycoprotein similarities from mass spectrometric data.

William Edwin Hackett, Joseph Zaia,

Complex protein glycosylation occurs through biosynthetic steps in the secretory pathway that create macro- and microheterogeneity of structure and function.  Required for all life forms, glycosylation diversifies and adapts protein interactions with binding partners that underpin interactions at cell surfaces and pericellular and extracellular environments. Because these biological effects arise ... Read more >>

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

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The Capture of a Disabled Proteasome Identifies Erg25 as a Substrate for Endoplasmic Reticulum Associated Degradation.

Teresa M Buck, Xuemei Zeng, Pamela S Cantrell, Richard T Cattley, Zikri Hasanbasri, Megan E Yates, Diep Nguyen, Nathan A Yates, Jeffrey L Brodsky,

Studies in the yeast Saccharomyces cerevisiae have helped define mechanisms underlying the activity of the ubiquitin-proteasome system (UPS), uncover the proteasome assembly pathway, and link the UPS to the maintenance of cellular homeostasis. However, the spectrum of UPS substrates is incompletely defined, even though multiple techniques-including mass spectrometry (MS)-have been ... Read more >>

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

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A comprehensive gender-related secretome of Plasmodium berghei sexual stages.

Felicia Grasso, Stefania Mochi, Federica Fratini, Anna Olivieri, Chiara Currà, Inga Siden-Kiamos, Elena Deligianni, Cecilia Birago, Leonardo Picci, Elisabetta Pizzi, Tomasino Pace, Marta Ponzi,

Plasmodium, the malaria parasite, undergoes a complex life cycle alternating between a vertebrate host and a mosquito vector of the genus Anopheles. In red blood cells of the vertebrate host, Plasmodium multiplies asexually or differentiates into gamete precursors, the male and female gametocytes, responsible for parasite transmission. Sexual stage maturation ... Read more >>

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

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Peak Filtering, Peak Annotation, and Wildcard Search for Glycoproteomics.

Abhishek Roushan, Gary M Wilson, Doron Kletter, K Ilker Sen, Wilfred H Tang, Yong J Kil, Eric Carlson, Marshall Bern,

Glycopeptides in peptide or digested protein samples pose a number of analytical and bioinformatics challenges beyond those posed by unmodified peptides or peptides with smaller posttranslational modifications. Exact structural elucidation of glycans is generally beyond the capability of a single mass spectrometry experiment, so a reasonable level of identification for ... Read more >>

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

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Citrus vascular proteomics highlights the role of peroxidases and serine proteases during Huanglongbing disease progression.

Jessica Franco, Shree P Thapa, Zhiqian Pang, Fatta B Gurung, Thomas W Liebrand, Danielle M Stevens, Veronica Ancona, Nian Wang, Gitta Coaker,

Huanglongbing (HLB) is the most devastating and widespread citrus disease. All commercial citrus varieties are susceptible to the HLB-associated bacterium, Candidatus Liberibacter asiaticus (CLas), which resides in the phloem. The phloem is part of the plant vascular system and is involved in sugar transport. To investigate the plant response to ... Read more >>

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

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A mouse brain-based multi-omics integrative approach reveals potential blood biomarkers for ischemic stroke.

Alba Simats, Laura Ramiro, Teresa García-Berrocoso, Ferran Briansó, Ricardo Gonzalo, Luna Martín, Anna Sabé, Natalia Gill, Anna Penalba, Nuria Colome, Alex Sánchez, Francesc Canals, Alejandro Bustamante, Anna Rosell, Joan Montaner,

Stroke remains a leading cause of death and disability worldwide. Despite continuous advances, the identification of key molecular signatures in the hyper-acute phase of ischemic stroke is still a primary interest for translational research on stroke diagnosis, prognosis, and treatment. Data integration from high-throughput -omics techniques has become crucial to ... Read more >>

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

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Glutathionylation decreases methyltransferase activity of PRMT5 and inhibits cell proliferation.

Meiqi Yi, Yingying Ma, Yuling Chen, Chongdong Liu, Qingtao Wang, Haiteng Deng,

Glutathionylation is an important posttranslational modification that protects proteins from further oxidative damage as well as influencing protein structure and activity. In the present study, we demonstrate that the cysteine-42 residue in protein arginine N-methyltransferase 5 (PRMT5) is glutathionylated in aged mice or in cells that have been exposed to ... Read more >>

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

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Single-Cell Proteomics: Progress and Prospects.

Ryan T Kelly,

MS-based proteome profiling has become increasingly comprehensive and quantitative, yet a persistent shortcoming has been the relatively large samples required to achieve an in-depth measurement. Such bulk samples, typically comprising thousands of cells or more, provide a population average and obscure important cellular heterogeneity. Single-cell proteomics capabilities have the potential ... Read more >>

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

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Sialylation of Asparagine 612 inhibits Aconitase activity during mouse sperm capacitation; A possible mechanism for the switch from oxidative phosphorylation to glycolysis.

Ana Izabel Silva Balbin Villaverde, Rachel A Ogle, Peter Lewis, Vincenzo Carbone, Tony Velkov, Jacob K Netherton, Mark A Baker,

After ejaculation, mammalian spermatozoa must undergo a process known as capacitation in order to successfully fertilize the oocyte. Several post-translational modifications occur during capacitation, including sialylation, which despite being limited to a few proteins, seems to be essential for proper sperm-oocyte interaction. Regardless of its importance, to date, no single ... Read more >>

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

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Multiomics reveals ectopic ATP synthase blockade induces cancer cell death via a lncRNA-mediated phospho-signaling network.

Yi-Wen Chang, Chia-Lang Hsu, Cheng-Wei Tang, Xiang-Jun Chen, Hsuan-Cheng Huang, Hsueh-Fen Juan,

The EGFR tyrosine kinase inhibitor gefitinib is commonly used for lung cancer patients. However, some patients eventually become resistant to gefitinib and develop progressive disease. Here, we indicate that ecto-ATP synthase, which ectopically translocated from mitochondrial inner membrane to plasma membrane, is considered as a potential therapeutic target for drug-resistant ... Read more >>

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

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Analytical guidelines for co-fractionation mass spectrometry obtained through global profiling of gold standard Saccharomyces cerevisiae protein complexes.

Chi Nam Ignatius Pang, Sara Ballouz, Daniel Weissberger, Loïc M Thibaut, Joshua J Hamey, Jesse Gillis, Marc R Wilkins, Gene Hart-Smith,

Co-fractionation mass spectrometry (CF-MS) is a technique with potential to characterise endogenous and unmanipulated protein complexes on an unprecedented scale. However this potential has been offset by a lack of guidelines for best-practice CF-MS data collection and analysis. To obtain such guidelines, this study thoroughly evaluates novel and published Saccharomyces ... Read more >>

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

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High-speed analysis of large sample sets - how can this key aspect of the omics be achieved?

Rainer Cramer,

High-speed analysis of large (prote)omics sample sets at the rate of thousands or millions of samples per day on a single platform has been a challenge since the beginning of proteomics. For many years, electrospray ionisation (ESI)-based mass spectrometry (MS) methods have dominated proteomics due to their high sensitivity and ... Read more >>

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

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Slight deuterium enrichment in water acts as an antioxidant: is deuterium a cell growth regulator?

Xuepei Zhang, Jin Wang, Roman A Zubarev,

Small admixtures in water, e.g. of metal ions, often act as cell growth regulators. Here we report that enrichment of deuterium content in water, normally found at 8 mM concentration, two-three folds increases cell proliferation and lowers the oxidative stress level as well. Acting as an anti-oxidant, deuterium-enriched water prevents ... Read more >>

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

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