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Molecular & Cellular Proteomics: MCP

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https://read.qxmd.com/read/30765458/conodipine-p1-3-the-first-phospholipases-a-2-characterized-from-injected-cone-snail-venom
#1
Carolina Moller, William Clay Davis, Evan Clark, Anthony De Caprio, Frank Mari
The phospholipase A2 (PLA2 s) superfamily are ubiquitous small enzymes that catalyze the hydrolysis of phospholipids at the sn-2 ester bond. PLA2 s in the venom of cone snails (conodipines, Cdpi) are composed of two chains termed as alpha and beta subunits. Conodipines are categorized within the group IX of PLA2 s. Here we describe the purification and biochemical characterization of three conodipines (Cdpi-P1, -P2 and -P3) isolated from the injected venom of Conus purpurascens. Using proteomics methods, we determined the full sequences of all three conodipines...
February 14, 2019: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/30760538/microvesicle-proteomic-profiling-of-uterine-liquid-biopsy-for-ovarian-cancer-early-detection
#2
Georgina D Barnabas, Keren Bahar-Shany, Stav Sapoznik, Limor Helpman, Yfat Kadan, Mario Beiner, Omer Weitzner, Nissim Arbib, Jacob Korach, Tamar Perri, Guy Katz, Anna Blecher, Benny Brandt, Eitan Friedman, David Stockheim, Ariella Jakobson-Setton, Ram Eitan, Shunit Armon, Hadar Brand, Oranit Zadok, Sarit Aviel-Ronen, Michal Harel, Tamar Geiger, Keren Levanon
High-grade ovarian cancer (HGOC) is the leading cause of mortality from gynecological malignancies, due to diagnosis at a metastatic stage. Current screening options fail to improve mortality due to the absence of early-stage-specific biomarkers. We postulated that a liquid biopsy, such as utero-tubal lavage (UtL), may identify localized lesions better than systemic approaches of serum/plasma analysis. Furthermore, while mutation-based assays are challenged by the rarity of tumor DNA within non-mutated DNA, analyzing the proteomic profile, is expected to enable earlier detection, as it reveals perturbations in both the tumor as well as in its microenvironment...
February 13, 2019: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/30760537/the-old-and-the-new-discovery-proteomics-identifies-putative-novel-seminal-fluid-proteins-in-drosophila
#3
Timothy L Karr, Helen Southern, Matthew A Rosenow, Toni I Gossmann, Rhonda R Snook
Seminal fluid proteins (SFPs), the non-sperm component of male ejaculates produced by male accessory glands, are viewed as central mediators of reproductive fitness. SFPs effect both male and female post-mating functions and show molecular signatures of rapid adaptive evolution. While Drosophila melanogaster is the dominant insect model for understanding SFP evolution, understanding of SFP evolutionary causes and consequences require additional comparative analyses of close and distantly-related taxa. While SFP identification was historically challenging, advances in label-free quantitative proteomics expands the scope of studying other systems to further advance the field...
February 13, 2019: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/30760536/for-the-sake-of-science
#4
Lila M Gierasch, Nicholas O Davidson, Kerry-Anne Rye, Alma L Burlingame
No abstract text is available yet for this article.
February 13, 2019: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/30755466/maxquant-live-enables-global-targeting-of-more-than-25-000-peptides
#5
Christoph Wichmann, Florian Meier, Sebastian Virreira Winter, Andreas-David Brunner, Jürgen Cox, Matthias Mann
Mass spectrometry (MS)-based proteomics is often performed in a shotgun format, in which as many peptide precursors as possible are selected from full or MS1 scans so that their fragment spectra can be recorded in MS2 scans. While achieving great proteome depths, shotgun proteomics cannot guarantee that each precursor will be fragmented in each run. In contrast, targeted proteomics aims to reproducibly and sensitively record a restricted number of precursor/fragment combinations in each run, based on pre-scheduled mass-to-charge and retention time windows...
February 12, 2019: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/30723094/probing-h-2-o-2-mediated-structural-dynamics-of-the-human-26s-proteasome-using-quantitative-cross-linking-mass-spectrometry-qxl-ms
#6
Clinton Yu, Xiaorong Wang, Alexander S Huszagh, Rosa Viner, Eric J Novitsky, Scott D Rychnovsky, Lan Huang
Cytotoxic protein aggregation-induced impairment of cell function and homeostasis are hallmarks of age-related neurodegenerative pathologies. As proteasomal degradation represents the major clearance pathway for oxidatively damaged proteins, a detailed understanding of the molecular events underlying its stress response is critical for developing strategies to maintain cell viability and function. Although the 26S proteasome has been shown to disassemble during oxidative stress, its conformational dynamics remains unclear...
February 5, 2019: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/30718293/immunomic-identification-of-malaria-antigens-associated-with-protection-in-mice
#7
Anthony Siau, Ximei Huang, Han Ping Loh, Neng Zhang, Wei Meng, Siu Kwan Sze, Laurent Renia, Peter R Preiser
Efforts to develop vaccines against malaria represent a major research target. The observations that 1) sterile protection can be obtained when the host is exposed to live parasites and 2) the immunity against blood stage parasite is principally mediated by protective antibodies suggest that a protective vaccine is feasible. However, only a small number of proteins have been investigated so far and most of the Plasmodium proteome has yet to be explored. To date, only few immunodominant antigens have emerged for testing in clinical trials but no formulation has led to substantial protection in humans...
February 4, 2019: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/30705125/quantitative-multiplex-substrate-profiling-of-peptidases-by-mass-spectrometry
#8
John D Lapek, Zhenze Jiang, Jacob M Wozniak, Elena Arutyunova, Steven C Wang, M Joanne Lemieux, David J Gonzalez, Anthony J O'Donoghue
Proteolysis is an integral component of life and has been implicated in many disease processes. To improve our understanding of peptidase function, it is imperative to develop tools to uncover substrate specificity and cleavage efficiency. Here, we combine the quantitative power of tandem mass tags (TMTs) with an established peptide cleavage assay to yield quantitative Multiplex Substrate Profiling by Mass Spectrometry (qMSP-MS). This assay was validated with papain, a well-characterized cysteine peptidase, to generate cleavage efficiency values for hydrolysis of 275 unique peptide bonds in parallel...
January 31, 2019: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/30705124/dialignr-provides-precise-retention-time-alignment-across-distant-runs-in-dia-and-targeted-proteomics
#9
Shubham Gupta, Sara Ahadi, Wenyu Zhou, Hannes Rost
SWATH-MS has been widely used for proteomics analysis given its high-throughput and reproducibility but ensuring consistent quantification of analytes across large-scale studies of heterogeneous samples such as human-plasma remains challenging. Heterogeneity in large-scale studies can be caused by large time intervals between data-acquisition, acquisition by different operators or instruments, intermittent repair or replacement of parts, such as the liquid chromatography column, all of which affect retention time (RT) reproducibility and successively performance of SWATH-MS data analysis...
January 31, 2019: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/30705123/integration-of-two-in-depth-quantitative-proteomics-approaches-determines-the-kallikrein-related-peptidase-7-klk7-degradome-in-ovarian-cancer-cell-secretome
#10
Lakmali Munasinghage Silva, Thomas Kryza, Thomas Stoll, Christine Hoogland, Ying Dong, Carson R Stephens, Marcus L Hastie, Viktor Magdolen, Oded Kleifeld, Jeffrey J Gorman, Judith Clements
Kallikrein-related peptidase 7 (KLK7) is a serine peptidase that is over expressed in ovarian cancer. In vitro functional analyses have suggested KLK7 to play a cancer progressive role, although monitoring of KLK7 expression has suggested a contradictory protective role for KLK7 in ovarian cancer patients. In order to help delineate its mechanism of action and thereby the functional roles, information on its substrate repertoire is crucial. Therefore, in this study a quantitative proteomics approach - PROtein TOpography and Migration Analysis Platform (PROTOMAP)-coupled with SILAC was used for in-depth analysis of putative KLK7 substrates from a representative ovarian cancer cell line, SKOV-3, secreted proteins...
January 31, 2019: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/30700495/mass-spectrometry-based-absolute-quantification-of-20s-proteasome-status-for-controlled-ex-vivo-expansion-of-human-adipose-derived-mesenchymal-stromal-stem-cells
#11
Thomas Menneteau, Bertrand Fabre, Luc Garrigues, Alexandre Stella, Dusan Zivkovic, Florence Roux-Dalvai, Emanuelle Mouton-Barbosa, Mathilde Beau, Marie-Laure Renoud, François Amalric, Luc Sensebe, Anne Gonzalez-de-Peredo, Isabelle Ader, Odile Burlet-Schiltz, Marie-Pierre Bousquet
The proteasome controls a multitude of cellular processes through protein degradation and has been identified as a therapeutic target in oncology. However, our understanding of its function and the development of specific modulators are hampered by the lack of a straightforward method to determine the overall proteasome status in biological samples. Here, we present a method to determine the absolute quantity and stoichiometry of ubiquitous and tissue-specific human 20S proteasome subtypes based on a robust, absolute SILAC-based multiplexed LC-Selected Reaction Monitoring (SRM) quantitative mass spectrometry assay with high precision, accuracy, and sensitivity...
January 30, 2019: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/30692274/identification-of-candidate-plasma-protein-biomarkers-for-cervical-cancer-using-the-multiplex-proximity-extension-assay
#12
Malin Berggrund, Stefan Enroth, Martin Lundberg, Erika Assarsson, Karin Stålberg, David Lindquist, Göran Hallmans, Kjell Grankvist, Matts Olovsson, Ulf Gyllensten
Human papillomavirus (HPV) is recommended as the primary test in cervical cancer screening, with co-testing by cytology for HPV-positive women to identify cervical lesions. Cytology has low sensitivity and there is a need to identify biomarkers that could identify dysplasia that are likely to progress to cancer. We searched for plasma proteins that could identify women with cervical cancer using the multiplex proximity extension assay (PEA). The abundance of 100 proteins were measured in plasma collected at the time of diagnosis of patients with invasive cervical cancer and in population controls using the Olink Multiplex panels CVD II, INF I, and ONC II...
January 28, 2019: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/30683686/human-testis-phosphoproteome-reveals-kinases-as-potential-targets-in-spermatogenesis-and-testicular-cancer
#13
Judit Castillo, Jaco C Knol, Cindy M Korver, Sander R Piersma, Thang V Pham, Richard R Goeij de Haas, Ans M M van Pelt, Connie R Jimenez, Bastiaan J H Jansen
Spermatogenesis is a complex cell differentiation process that includes marked genetic, cellular, functional and structural changes. It requires tight regulation, since disturbances in any of the spermatogenic processes would lead to fertility deficiencies as well as disorders in offspring. In order to increase our knowledge of signal transduction during sperm development, we carried out a large-scale identification of the phosphorylation events that occur in the human male gonad. Metal oxide affinity chromatography using TiO2combined with LC-MS/MS was conducted to profile the phosphoproteome of adult human testes with full spermatogenesis...
January 25, 2019: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/30679258/investigating-lactococcus-lactis-mg1363-response-to-phage-p2-infection-at-the-proteome-level
#14
Marie-Laurence Lemay, Andreas Otto, Sandra Maaß, Kristina Plate, Dörte Becher, Sylvain Moineau
Phages are viruses that specifically infect and eventually kill their bacterial hosts. Bacterial fermentation and biotechnology industries see them as enemies, however, they are also investigated as antibacterial agents for the treatment or prevention of bacterial infections in various sectors. They also play key ecological roles in all ecosystems. Despite decades of research some aspects of phage biology are still poorly understood. In this study, we used label-free quantitative proteomics to reveal the proteotypes of Lactococcus lactis MG1363 during infection by the virulent phage p2, a model for studying the biology of phages infecting Gram-positive bacteria...
January 24, 2019: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/30659065/multi-isotype-glycoproteomic-characterization-of-serum-antibody-heavy-chains-reveals-isotype-and-subclass-specific-n-glycosylation-profiles
#15
Kevin Brown Chandler, Nickita Mehta, Deborah R Leon, Todd Suscovich, Galit Alter, Catherine E Costello
Antibodies are critical glycoproteins that bridge the innate and adaptive immune systems to provide protection against infection. The isotype/subclass of the antibody, the co-translational N -glycosylation on the CH2 domain, and the remodeling of the N -linked glycans during passage through the ER and Golgi are the known variables within the Fc domain that program antibody effector function. Through investigations of monoclonal therapeutics, it has been observed that addition or removal of specific monosaccharide residues from antibody N -glycans can influence the potency of antibodies, highlighting the importance of thoroughly characterizing antibody N -glycosylation...
January 18, 2019: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/30659061/apolipoprotein-a1-forms-5-5-and-5-4-antiparallel-dimers-in-human-high-density-lipoprotein
#16
Yi He, Hyun D Song, G M Anantharamaiah, M N Palgunachari, Karin Bornfeldt, Jere P Segrest, Jay Heinecke
Apolipoprotein A1 (APOA1), the major protein of high-density lipoprotein (HDL), contains 10 helical repeats that play key roles in protein-protein and protein-lipid interactions. The current structural model for HDL proposes that APOA1 forms an antiparallel dimer in which helix 5 in monomer 1 associates with helix 5 in monomer 2 along a left-left (LL5/5) interface, forming a protein complex with a two-fold axis of symmetry centered on helix 5. However, computational studies suggest that other orientations are possible...
January 18, 2019: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/30651306/data-independent-acquisition-improves-quantitative-cross-linking-mass-spectrometry
#17
Fränze Müller, Lars Kolbowski, Oliver M Bernhardt, Lukas Reiter, Juri Rappsilber
Quantitative cross-linking mass spectrometry (QCLMS) reveals structural detail on altered protein states in solution. On its way to becoming a routine technology, QCLMS could benefit from data-independent acquisition (DIA), which generally enables greater reproducibility than data-dependent acquisition (DDA) and increased throughput over targeted methods. Therefore, here we introduce DIA to QCLMS by extending a widely used DIA software, Spectronaut, to also accommodate cross-link data. A mixture of seven proteins cross-linked with bis[sulfosuccinimidyl] suberate (BS3) was used to evaluate this workflow...
January 16, 2019: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/30647073/accurate-estimation-of-context-dependent-false-discovery-rates-in-top-down-proteomics
#18
Richard D LeDuc, Ryan T Fellers, Bryan P Early, Joseph B Greer, Daniel P Shams, Paul Thomas, Neil L Kelleher
Within the last several years, top-down proteomics has emerged as a high throughput technique for protein and proteoform identification. This technique has the potential to identify and characterize thousands of proteoforms within a single study, but the absence of accurate false discovery rate (FDR) estimation could hinder the adoption and consistency of top-down proteomics in the future. In automated identification and characterization of proteoforms, FDR calculation strongly depends on the context of the search...
January 15, 2019: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/30635358/macrophage-phosphoproteome-analysis-reveals-mincle-dependent-and-independent-mycobacterial-cord-factor-signaling
#19
Madlen Hansen, Julien Peltier, Barbara Killy, Bushra Amin, Barbara Bodendorfer, Anetta Härtlova, Sebastian Uebel, Markus Bosmann, Jörg Hofmann, Christian Büttner, Arif B Ekici, Mario Kuttke, Henrik Franzyk, Camilla Foged, Sandra Beer-Hammer, Gernot Schabbauer, Matthias Trost, Roland Lang
Immune sensing of Mycobacterium tuberculosis relies on recognition by macrophages. Mycobacterial cord factor, trehalose-6,6'-dimycolate (TDM), is the most abundant cell wall glycolipid and binds to the C-type lectin receptor (CLR) MINCLE. To explore the kinase signaling linking the TDM-MINCLE interaction to gene expression, we employed quantitative phosphoproteome analysis. TDM caused upregulation of 6.7% and suppressed 3.8% of the 14,000 phospho-sites identified on 3727 proteins. MINCLE-dependent phosphorylation was observed for canonical players of CLR signaling (e...
January 11, 2019: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/30630937/proteome-analysis-of-human-neutrophil-granulocytes-from-patients-with-monogenic-disease-using-data-independent-acquisition
#20
Piotr Grabowski, Sebastian Hesse, Sebastian Hollizeck, Meino Rohlfs, Uta Behrends, Roya Sherkat, Hannah Tamary, Ekrem Ünal, Raz Somech, Türkan Patıroğlu, Stefan Canzar, Jutte van der Werff Ten Bosch, Christoph Klein, Juri Rappsilber
Neutrophil granulocytes are critical mediators of innate immunity and tissue regeneration. Rare diseases of neutrophil granulocytes may affect their differentiation and/or functions. However, there are very few validated diagnostic tests assessing the functions of neutrophil granulocytes in these diseases. Here, we set out to probe omics analysis as a novel diagnostic platform for patients with defective differentiation and function of neutrophil granulocytes. We analyzed highly purified neutrophil granulocytes from 68 healthy individuals and 16 patients with rare monogenic diseases...
January 10, 2019: Molecular & Cellular Proteomics: MCP
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