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Molecular & Cellular Proteomics: MCP

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https://www.readbyqxmd.com/read/28432195/n-terminal-proteomics-assisted-profiling-of-the-unexplored-translation-initiation-landscape-in-arabidopsis-thaliana
#1
Patrick Willems, Elvis Ndah, Veronique Jonckheere, Simon Stael, Adriaan Sticker, Lennart Martens, Frank Van Breusegem, Kris Gevaert, Petra Van Damme
Proteogenomics is an emerging research field yet lacking a uniform method of analysis. Proteogenomic studies in which N-terminal proteomics and ribosome profiling are combined, suggest that a high number of protein start sites are currently missing in genome annotations. We constructed a proteogenomic pipeline specific for the analysis of N-terminal proteomics data, with the aim of discovering novel translational start sites outside annotated protein coding regions. In summary, unidentified MS/MS spectra were matched to a specific N-terminal peptide library encompassing protein N-termini encoded in the Arabidopsis thaliana genome...
April 21, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28428241/heralds-of-parallel-ms-data-independent-acquisition-surpassing-sequential-identification-of-data-dependent-acquisition-in-proteomics
#2
Roland Bruderer, Oliver Martin Bernhardt, Tejas Gandhi, Yue Xuan, Julia Sondermann, Manuela Schmidt, David Gomez-Varela, Lukas Reiter
Comprehensive, reproducible and precise analysis of large sample cohorts is one of the key objectives of quantitative proteomics. Here, we present an implementation of data-independent acquisition using its parallel acquisition nature that surpasses the serial limitation of data-dependent acquisition on a quadrupole ultra-high field Orbitrap mass spectrometer. In deep single shot data-independent acquisition, we quantified over 7,500 proteins of human cell lines and 9,000 proteins of mouse tissues, with fewer than 2...
April 20, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28420677/tcup-typing-and-characterization-of-bacteria-using-bottom-up-tandem-mass-spectrometry-proteomics
#3
Fredrik Boulund, Roger Karlsson, Lucia Gonzales-Siles, Anna Johnning, Nahid Karami, Omar Al-Bayati, Christina Ahren, Edward R B Moore, Erik Kristiansson
Methods for rapid and reliable microbial identification are essential in modern healthcare. The ability to detect and correctly identify pathogenic species and their resistance phenotype is necessary for accurate diagnosis and efficient treatment of infectious diseases. Bottom-up tandem mass spectrometry (MS) proteomics enables rapid characterization of large parts of the expressed genes of microorganisms. However, the generated data is highly fragmented, making down-stream analyses complex. Here we present TCUP, a new computational method for typing and characterizing bacteria using proteomics data from bottom-up tandem MS...
April 18, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28416578/quantitative-mass-spectrometry-analysis-of-pd-l1-protein-expression-n-glycosylation-and-expression-stoichiometry-with-pd-1-and-pd-l2-in-human-melanoma
#4
Carlos A Morales-Betanzos, Hyoungjoo Lee, Paula I Gonzalez-Ericsson, Justin M Balko, Douglas B Johnson, Lisa J Zimmerman, Daniel C Liebler
Quantitative assessment of key proteins that control the tumor-immune interface is one of the most formidable analytical challenges in immunotherapeutics. We developed a targeted mass spectrometry (MS) platform to quantify programmed cell death-1 (PD-1), programmed cell death 1 ligand 1 (PD-L1), and programmed cell death 1 ligand 2 (PD-L2) at fmol/microgram protein levels in formalin fixed, paraffin-embedded sections from 22 human melanomas. PD-L1 abundance ranged 50-fold, from approximately 0.03 to 1.5 fmol/microgram protein and the PRM data were largely concordant with total PD-L1-positive cell content, as analyzed by immunohistochemistry (IHC) with the E1L3N antibody...
April 17, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28408662/the-gdnf-responsive-phosphoprotein-landscape-identifies-raptor-phosphorylation-required-for-spermatogonial-progenitor-cell-proliferation
#5
Min Wang, Yueshuai Guo, Mei Wang, Tao Zhou, Yuanyuan Xue, Guihua Du, Xiang Wei, Jing Wang, Lin Qi, Hao Zhang, Lufan Li, Lan Ye, Xuejiang Guo, Xin Wu
Cytokine-dependent renewal of stem cells is a fundamental requisite for tissue homeostasis and regeneration. Spermatogonial progenitor cells (SPCs) including stem cells support life-long spermatogenesis and male fertility, but pivotal phosphorylation events that regulate fate decisions in SPCs remain unresolved. Here, we described a quantitative mass-spectrometry-based proteomic and phosphoproteomic analyses of SPCs following sustained stimulation with glial cell-derived neurotrophic factor (GDNF), an extrinsic factor supporting SPC proliferation...
April 13, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28404795/dynamics-of-the-interaction-between-cotton-bollworm-helicoverpa-armigera-and-nucleopolyhedrovirus-as-revealed-by-integrated-transcriptomic-and-proteomic-analyses
#6
Longsheng Xing, Chuanfei Yuan, Manli Wang, Zhe Lin, Benchang Shen, Zhihong Hu, Zhen Zou
Over the past decades, Helicoverpa armigera nucleopolyhedrovirus (HearNPV) has been widely used for biocontrol of cotton bollworm, which is one of the most destructive pest insects in agriculture worldwide. However, the molecular mechanism underlying the interaction between HearNPV and host insects remains poorly understood. In this study, high throughput RNA-sequencing was integrated with label-free quantitative proteomics analysis to examine the dynamics of gene expression in the fat body of H. armigera larvae in response to challenge with HearNPV...
April 12, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28404794/neprosin-a-selective-prolyl-endoprotease-for-bottom-up-proteomics-and-histone-mapping
#7
Christoph U Schraeder, Linda Lee, Martial Rey, Vladimir Sarpe, Petr Man, Seema Sharma, Vlad Zabrouskov, Brett Larsen, David C Schriemer
Trypsin dominates bottom-up proteomics, but there are reasons to consider alternative enzymes. Improving sequence coverage, exposing proteomic dark matter and clustering post-translational modifications in different ways and with higher-order drive the pursuit of reagents complementary to trypsin. Additionally, enzymes that are easy to use and generate larger peptides that capitalize upon newer fragmentation technologies should have a place in proteomics. We expressed and characterized recombinant neprosin, a novel prolyl endoprotease of the DUF239 family, which preferentially cleaves C-terminal to proline residues under highly acidic conditions...
April 12, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28396511/a-database-augmented-exosome-based-mass-spectrometry-approach-exemplarily-identifies-circulating-claudin-3-as-biomarker-in-prostate-cancer
#8
Thomas Stefan Worst, Jost von Hardenberg, Julia Christina Gross, Philipp Erben, Martina Schnoelzer, Ingrid Hausser, Peter Bugert, Maurice Stephan Michel, Michael Boutros
In prostate cancer and other malignancies sensitive and robust biomarkers are lacking or have relevant limitations. Prostate specific antigen (PSA), the only biomarker widely used in prostate cancer, is suffering from low specificity. Exosomes offer new perspectives in the discovery of blood-based biomarkers. Here we present a proof-of principle study for a proteomics-based identification pipeline, implementing existing data sources, to exemplarily identify exosome-based biomarker candidates in prostate cancer...
April 9, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28389583/development-of-large-scale-cross-linking-mass-spectrometry
#9
Helena Maria Barysz, Johan Malmstroem
Cross-linking mass spectrometry (CLMS) provides distance constraints to study the structure of proteins, multiprotein complexes and protein-protein interactions which are critical for the understanding of protein function. CLMS is an attractive technology to bridge the gap between high-resolution structural biology techniques and proteomic-based interactome studies. However, as outlined in this review there are still several bottlenecks associated with CLMS which limit its application on a proteome-wide level...
April 7, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28385878/protease-inhibitor-interaction-predictions-lessons-on-the-complexity-of-protein-protein-interactions
#10
Nikolaus Fortelny, Georgina S Butler, Christopher Mark Overall, Paul Pavlidis
Protein interactions shape proteome function and thus biology. Identification of protein interactions is a major goal in molecular biology, but biochemical methods, although improving, remain limited in coverage and accuracy. Whereas computational predictions can guide biochemical experiments, low validation rates of predictions remain a major limitation. Here, we investigated computational methods in the prediction of a specific type of interaction, the inhibitory interactions between proteases and their inhibitors...
April 6, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28373298/mob1-mediated-phospho-recognition-in-the-core-mammalian-hippo-pathway
#11
Amber L Couzens, Shawn Xiong, James Dr Knight, Daniel Y Mao, Sebastian Guettler, Sarah Picaud, Igor Kurinov, Panagis Filippakopoulos, Frank Sicheri, Anne-Claude Gingras
The Hippo tumor suppressor pathway regulates organ size and tissue homoeostasis in response to diverse signaling inputs. The core of the pathway consists of a short kinase cascade: MST1 and MST2 phosphorylate and activate LATS1 and LATS2, which in turn phosphorylate and inactivate key transcriptional co-activators, YAP1 and TAZ (gene WWTR1). The MOB1 adapter protein regulates both phosphorylation reactions firstly by concurrently binding to the upstream MST and downstream LATS kinases to enable the trans phosphorylation reaction, and secondly by allosterically activating the catalytic function of LATS1 and LATS2 to directly stimulate phosphorylation of YAP and TAZ...
April 3, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28373297/regulation-of-protein-interactions-by-mob1-phosphorylation
#12
Shawn Xiong, Amber L Couzens, Michelle J Kean, Daniel Y Mao, Sebastian Guettler, Igor Kurinov, Anne-Claude Gingras, Frank Sicheri
MOB1 is a multifunctional protein best characterized for its integrative role in regulating Hippo and NDR pathway signaling in metazoans and the Mitotic Exit Network in yeast. Human MOB1 binds both the upstream kinases MST1 and MST2 and the downstream AGC group kinases LATS1, LATS2, NDR1 and NDR2. Binding of MOB1 to MST1 and MST2 is mediated by its phosphopeptide-binding infrastructure, the specificity of which matches the phosphorylation consensus of MST1 and MST2. On the other hand, binding of MOB1 to the LATS and NDR kinases is mediated by a distinct interaction surface on MOB1...
April 3, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28373296/a-proteomic-approach-to-identify-alterations-in-the-sumo-network-during-controlled-mechanical-ventilation-in-rat-diaphragm-muscle
#13
Arvind Venkat Namuduri, Gabriel Heras, Jia Mi, Nicola Cacciani, Katarina Hörnaeus, Anne Konzer, Sara Bergström Lind, Lars Larsson, Stefano Gastaldello
The Small Ubiquitin-like Modifier (SUMO) is as a regulator of many cellular functions by reversible conjugation to a broad number of substrates. Under endogenous or exogenous perturbations, the SUMO network becomes a fine sensor of stress conditions by alterations in the expression level of SUMO enzymes and consequently changing the status of SUMOylated proteins. The diaphragm is the major inspiratory muscle, which is continuously active under physiological conditions, but its structure and function is severely affected when passively displaced for long extents during mechanical ventilation (MV)...
April 3, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28373295/proteomic-analysis-of-regulatory-t-cells-reveals-the-importance-of-themis1-in-the-control-of-their-suppressive-function
#14
Fanny Duguet, Marie Locard-Paulet, Marlène Marcellin, Karima Chaoui, Isabelle Bernard, Olivier Andreoletti, Renaud Lesourne, Odile Burlet-Schiltz, Anne Gonzalez de Peredo, Abdelhadi Saoudi
Regulatory T cells (Treg) represent a minor sub-population of T lymphocytes which is crucial for the maintenance of immune homeostasis. Here, we present a large-scale quantitative mass spectrometry study that defines a specific proteomic signature of Treg. Treg and conventional T lymphocyte (Tconv) sub-populations were sorted by flow cytometry and subjected to global proteomic analysis by single-run nanoLC-MS/MS on a fast-sequencing Q-Exactive mass spectrometer. Besides historical proteins that characterize Treg, our study identified numerous new proteins that are up- or down-regulated in Treg versus Tconv...
April 3, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28348172/database-independent-protein-sequencing-dips-enables-full-length-de-novo-protein-and-antibody-sequence-determination
#15
Alon Savidor, Rotem Barzilay, Dalia Elinger, Yosef Yarden, Moshit Lindzen, Alexandra Gabashvili, Ophir Adiv Tal, Yishai Levin
Traditional 'bottom-up' proteomics approaches use proteolytic digestion, LC-MS/MS and database searching to elucidate peptide identities and their parent proteins. Protein sequences absent from the database cannot be identified, and even if present in the database, complete sequence coverage is rarely achieved even for the most abundant proteins in the sample. Thus, sequencing of unknown proteins such as antibodies or constituents of metaproteomes remains a challenging problem. To date, there is no available method for full-length protein sequencing, independent of a reference database, in high throughput...
March 27, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28348171/the-identification-of-macrophage-enriched-glycoproteins-using-glycoproteomics
#16
Jelani C Zarif, Weiming Yang, James R Hernandez, Hui Zhang, Kenneth J Pienta
Prostate cancer is a leading cause of cancer-related deaths of men in the U.S. While localized disease is highly treatable by surgical resection and radiation, cancer that has metastasized remains incurable. Immune cells that primarily scavenge debris, promote prostate cancer angiogenesis and wound repair are M2 Macrophages. They are phenotypically similar to M2 tumor-associated macrophages (M2-TAMs) have been reported to associate with solid tumors and aide in proliferation, metastasis, and resistance to therapy...
March 27, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28336726/proteomic-signature-of-acute-liver-failure-from-discovery-and-verification-in-a-pig-model-to-confirmation-in-humans
#17
Jie Wang, Zeyu Sun, Jing Jiang, Daxian Wu, Xiaoli Liu, Zhongyang Xie, Ermei Chen, Danhua Zhu, Chao Ye, Xiaoqian Zhang, Wenqian Chen, Hongcui Cao, Lanjuan Li
Acute liver failure (ALF) is a fatal condition hallmarked by rapid development. The present study aimed to describe the dynamic alterations of serum proteins associated with ALF development, and to seek for novel biomarkers of ALF. Miniature pigs (n=30) were employed to establish ALF models by infusing D-galactosamine (GALN, 1.3g/kg). A total of 1589 serum proteins were compared in pooled serum samples (n=10) before and 36 hours after GALN administration through label-free quantitation (LFQ) based shotgun proteomics...
March 23, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28336725/quantitative-shotgun-proteomics-unveils-candidate-novel-oesophageal-adenocarcinoma-specific-proteins
#18
J Robert O'Neill, Hui-Song Pak, Erola Pairo-Castineira, Vicki Save, Simon Paterson-Brown, Rudolf Nenutil, Bořivoj Vojtěšek, Ian Overton, Alex Scherl, Ted R Hupp
Oesophageal cancer is the eighth most common cancer worldwide and the majority of patients have systemic disease at presentation. Oesophageal adenocarcinoma (OAC), the predominant subtype in western countries, is largely resistant to current chemotherapy regimens. Selective markers are needed to enhance clinical staging and to allow targeted therapies yet there are minimal proteomic data on this cancer type. After histological review, lysates from OAC and matched normal oesophageal and gastric samples from seven patients were subjected to LC MS/MS after tandem mass tag labelling and OFFGEL fractionation...
March 23, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28336724/quantitative-age-specific-variability-of-plasma-proteins-in-healthy-neonates-children-and-adults
#19
Stefan Bjelosevic, Dana Pascovici, Hui Ping, Vasiliki Karlaftis, Thiri Zaw, Xiaomin Song, Mark P Molloy, Paul Monagle, Vera Ignjatovic
Human blood plasma is a complex biological fluid containing soluble proteins, sugars, hormones, electrolytes, and dissolved gasses. As plasma interacts with a wide array of bodily systems, changes in protein expression, or the presence or absence of specific proteins are regularly used in the clinic as a molecular biomarker tool. A large body of literature exists detailing proteomic changes in pathologic contexts, however little research has been conducted on the quantitation of the plasma proteome in age-specific, healthy subjects, especially in pediatrics...
March 23, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28336715/monitoring-cell-surface-n-glycoproteome-dynamics-by-quantitative-proteomics-reveals-mechanistic-insights-into-macrophage-differentiation
#20
Mathias Kalxdorf, Stephan Gade, H Christian Eberl, Marcus Bantscheff
The plasma membrane proteome plays a crucial role in inter- and intracellular signaling, cell survival and cell identity. As such it is a prominent target for pharmacological intervention. The relatively low abundance of this subproteome in conjunction with challenging extractability and solubility still hampers their comprehensive analysis. Here, we combined a chemical glycoprotein tagging strategy with mass spectrometry to enable comprehensive analysis of the cell surface glycoprotome. To benchmark this workflow and provide guidance for cell line selection for functional experiments, we generated an inventory of the N-linked cell surface glycoproteome of 15 standard laboratory human cell lines and three primary lymphocytic cell types...
March 23, 2017: Molecular & Cellular Proteomics: MCP
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