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Molecular & Cellular Proteomics: MCP

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https://www.readbyqxmd.com/read/28515314/the-mzidentml-data-standard-version-1-2-supporting-advances-in-proteome-informatics
#1
Juan Antonio Vizcaíno, Gerhard Mayer, Simon R Perkins, Harald Barsnes, Marc Vaudel, Yasset Perez-Riverol, Tobias Ternent, Julian Uszkoreit, Martin Eisenacher, Lutz Fischer, Juri Rappsilber, Eugen Netz, Mathias Walzer, Oliver Kohlbacher, Alexander Leitner, Robert J Chalkley, Fawaz Ghali, Salvador Martínez-Bartolomé, Eric W Deutsch, Andrew R Jones
The first stable version of the Proteomics Standards Initiative mzIdentML open data standard (version 1.1) was published in 2012 - capturing the outputs of peptide and protein identification software. In the intervening years, the standard has become well supported in both commercial and open software, as well as a submission and download format for public repositories. Here we report a new release of mzIdentML (version 1.2) that is required to keep pace with emerging practice in proteome informatics. New features have been added to support: (i) scores associated with localization of modifications on peptides; (ii) statistics performed at the level of peptides; (iii) identification of cross-linked peptides; and (iv) support for proteogenomics approaches...
May 17, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28512230/differential-proteomic-analysis-of-gender-dependent-hepatic-tumorigenesis-in-hras12v-transgenic-mice
#2
Zhuona Rong, Tingting Fan, Huiling Li, Juan Li, Kangwei Wang, Xinxin Wang, Jianyi Dong, Jun Chen, Fujin Wang, Jingyu Wang, Aiguo Wang
Male prevalence is an outstanding characteristic of hepatocellular carcinoma (HCC), and the underlying mechanisms for this have remained largely unknown. In the present study, Hras12V transgenic mice, in which hepatocyte-specific expression of the ras oncogene induces male-biased hepatic tumorigenesis, were studied, and altered proteins were detected by two-dimensional fluorescence difference gel electrophoresis (2D-DIGE). Protein samples from hepatic tumor tissues (T) and peri-tumor tissues (P) of transgenic males and females and the corresponding normal liver tissues (Wt) of non-transgenic males and females were subjected to pairwise comparisons based on proteomic analysis...
May 16, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28501802/stability-of-proteins-in-dried-blood-spot-biobanks
#3
Johan Björkesten, Stefan Enroth, Qiujin Shen, Lotta Wik, David Hougaard, Arieh Cohen, Lene Sörensen, Vilmantas Giedraitis, Martin Ingelsson, Anders Larsson, Masood Kamali-Moghaddam, Ulf Landegren
An important motivation for the construction of biobanks is to discover biomarkers that identify diseases at early, potentially curable stages. This will require biobanks from large numbers of individuals, preferably sampled repeatedly, where the samples are collected and stored under conditions that preserve potential biomarkers. Dried blood samples are attractive for biobanking because of the ease and low cost of collection and storage. Here we have investigated their suitability for protein measurements...
May 13, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28500030/translating-divergent-environmental-stresses-into-a-common-proteome-response-through-hik33-in-a-model-cyanobacterium
#4
Haitao Ge, Longfa Fang, Xiahe Huang, Jinlong Wang, Weiyang Chen, Ye Liu, Yuanya Zhang, Xiaorong Wang, Wu Xu, Qingfang He, Yingchun Wang
The histidine kinase Hik33 plays important roles in mediating cyanobacterial response to divergent types of abiotic stresses including cold, salt, high light (HL), and osmotic stresses. However, how these functions are regulated by Hik33 remains to be addressed. Using a hik33-deficient strain (Δhik33) of Synechocystis sp. PCC 6803 (Synechocystis) and quantitative proteomics, we found that Hik33 depletion induces differential protein expression highly similar to that induced by divergent types of stresses. This typically includes downregulation of proteins in photosynthesis and carbon assimilation that are necessary for cell propagation, and upregulation of heat shock proteins, chaperons, and proteases that are important for cell survival...
May 12, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28490445/serological-epithelial-component-proteins-identify-intestinal-complications-in-crohn-s-disease
#5
Yunki Y Yau, Rupert Wl Leong, Aviv Pudipeddi, Diane Redmond, Valerie C Wasinger
Crohns Disease (CD) is a relapsing inflammation of the gastrointestinal tract that affects a young working age population and is increasing in developing countries. Half of all sufferers will experience stricturing or fistulizing intestinal complications that require extensive surgical interventions and neither genes nor clinical risk factors can predict this debilitating natural history. We applied discovery and verification phase studies as part of an NCI-FDA modelled biomarker pipeline to identify differences in the low-mass (<25kDa) blood-serum proteome between CD behavioural phenotypes...
May 10, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28483926/some-gram-negative-lipoproteins-keep-their-surface-topology-when-transplanted-from-one-species-to-another-and-deliver-foreign-polypeptides-to-the-bacterial-surface
#6
Laura Fantappiè, Carmela Irene, Micaela De Santis, Alessandro Armini, Assunta Gagliardi, Michele Tomasi, Matteo Parri, Valeria Cafardi, Serena Bonomi, Luisa Ganfini, Francesca Zerbini, Ilaria Zanella, Chiara Carnemolla, Luca Bini, Alberto Grandi, Guido Grandi
In Gram-negative bacteria, outer membrane-associated lipoproteins can either face the periplasm or protrude out of the bacterial surface. The mechanisms involved in lipoprotein transport through the outer membrane are not fully elucidated. Some lipoproteins reach the surface by using species-specific transport machinery. By contrast, a still poorly characterized group of lipoproteins appears to always cross the outer membrane, even when transplanted from one organism to another. To investigate such lipoproteins, we tested the expression and compartmentalization in E...
May 8, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28483925/msstatsqc-longitudinal-system-suitability-monitoring-and-quality-control-for-targeted-proteomic-experiments
#7
Eralp Dogu, Sara Mohammad-Taheri, Susan E Abbatiello, Michael S Bereman, Brendan MacLean, Birgit Schilling, Olga Vitek
Selected Reaction Monitoring (SRM) is a powerful tool for targeted detection and quantification of peptides in complex matrices. An important objective of SRM is to obtain peptide quantifications that are (1) suitable for the purpose of the investigation, and (2) reproducible across laboratories and runs. The first objective is achieved by system suitability tests (SST), which verify that mass spectrometric instrumentation performs as specified. The second objective is achieved by quality control (QC), which provides in-process quality assurance of the sample profile...
May 8, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28456751/methods-tools-and-current-perspectives-in-proteogenomics
#8
Kelly V Ruggles, Karsten Krug, Xiaojing Wang, Karl R Clauser, Jing Wang, Samuel H Payne, David Fenyö, Bing Zhang, D R Mani
With combined technological advancements in high-throughput next-generation sequencing and deep mass spectrometry-based proteomics, proteogenomics, i.e., the integrative analysis of proteomic and genomic data, has emerged as a new research field. Early efforts in the field were focused on improving protein identification using sample-specific genomic and transcriptomic sequencing data. More recently, integrative analysis of quantitative measurements from genomic and proteomic studies have identified novel insights into gene expression regulation, cell signaling, and disease...
April 29, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28455291/hyper-phosphorylation-of-sequestosome-1-distinguishes-resistance-to-cisplatin-in-patient-derived-high-grade-serous-ovarian-cancer-cells
#9
Elizabeth V Nguyen, Kaisa Huhtinen, Young Ah Goo, Katja Kaipio, Noora Andersson, Ville Rantanen, Johanna Hynninen, Riitta Lahesmaa, Olli Carpen, David R Goodlett
Platinum-resistance is a major limitation to effective chemotherapy regimens in high-grade serous ovarian cancer (HGSOC). To better understand the mechanisms involved we characterized the proteome and phosphoproteome in cisplatin sensitive and resistant HGSOC primary cells using a mass spectrometry-based proteomic strategy. PCA analysis identified a distinctive phosphoproteomic signature between cisplatin sensitive and resistant cell lines. The most phosphorylated protein in cisplatin resistant cells was sequestosome-1 (p62/SQSTM1)...
April 28, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28450421/the-landscape-of-histone-modifications-in-a-high-fat-diet-induced-obese-dio-mouse-model
#10
Litong Nie, Lin Shuai, Mingrui Zhu, Ping Liu, Zhi-Fu Xie, Shangwen Jiang, Hao-Wen Jiang, Jia Li, Yingming Zhao, Jing-Ya Li, Minjia Tan
Type 2 diabetes (T2D) is a major chronic healthcare concern worldwide. Emerging evidence suggests that a histone-modification-mediated epigenetic mechanism underlies T2D. Nevertheless, the dynamics of histone marks in T2D have not yet been carefully analyzed. Using a mass spectrometry-based label-free and chemical stable isotope labeling quantitative proteomic approach, we systematically profiled liver histone post-translational modifications (PTMs) in a prediabetic high-fat-diet-induced obese (DIO) mouse model...
April 27, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28450420/validation-identification-and-biological-consequences-of-the-site-specific-o-glcnacylation-dynamics-of-chrebp
#11
An-Qi Yang, Daoyuan Li, Lianli Chi, Xin-Shan Ye
O-GlcNAcylation of carbohydrate-responsive element-binding protein (ChREBP) is believed as an important modulator of ChREBP activities, however little direct evidence of O-GlcNAcylation on ChREBP and no exact O-GlcNAcylation sites have been reported so far. Here, we validate O-GlcNAcylation on ChREBP in cell-free coupled transcription/translation system and in cells by chemoenzymatic and metabolic labeling, respectively. Moreover, for the first time, we identify O-GlcNAcylation on Ser614 in the C-terminus of ChREBP by mass spectrometry and validate two important sites, Thr517 and Ser839 for O-GlcNAcylation and their function via molecular and chemical biological method...
April 27, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28450419/phosphoproteome-analysis-reveals-differential-mode-of-action-of-sorafenib-in-wildtype-and-mutated-flt3-aml-cells
#12
Catrin Roolf, Nikolaj Dybowski, Anett Sekora, Stefan Mueller, Gudrun Knuebel, Andreas Tebbe, Hugo Murua Escobar, Klaus Godl, Christian Junghanss, Christoph Schaab
Constitutively activating internal tandem duplication (ITD) alterations of the receptor tyrosine kinase FLT3 (Fms-like tyrosine kinase 3) are common in acute myeloid leukemia (AML) and classifies FLT3 as an attractive therapeutic target. So far, applications of FLT3 small molecule inhibitors have been investigated primarily in FLT3-ITD+ patients. Only recently, a prolonged event-free survival has been observed in AML patients who were treated with the multi-kinase inhibitor sorafenib in addition to standard therapy...
April 27, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28432195/n-terminal-proteomics-assisted-profiling-of-the-unexplored-translation-initiation-landscape-in-arabidopsis-thaliana
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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