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A reference peptide database for proteome quantification based on experimental mass spectrum response curves

Wanlin Liu, Lai Wei, Jianan Sun, Jinwen Feng, Gaigai Guo, Lizhu Liang, Tianyi Fu, Mingwei Liu, Kai Li, Yin Huang, Weimin Zhu, Bei Zhen (+4 others)
2018 Bioinformatics  
Results: We constructed a reference database for proteome quantification based on experimental mass spectrum response curves.  ...  This study provides a reference database as well as a peptides/transitions selection method for quantitative proteomics.  ...  Jie Ma for advice on protein quantification, and Dr. Tao Chen for advice on web server development.  ... 
doi:10.1093/bioinformatics/bty201 pmid:29617941 pmcid:PMC6084618 fatcat:w3xhljj6xzhplfsuypxbnxokh4

ProteomicsDB

Tobias Schmidt, Patroklos Samaras, Martin Frejno, Siegfried Gessulat, Maximilian Barnert, Harald Kienegger, Helmut Krcmar, Judith Schlegl, Hans-Christian Ehrlich, Stephan Aiche, Bernhard Kuster, Mathias Wilhelm
2017 Nucleic Acids Research  
ProteomicsDB (https://www.ProteomicsDB.org) is a protein-centric in-memory database for the exploration of large collections of quantitative mass spectrometry-based proteomics data.  ...  The extended functionality transforms ProteomicsDB into a multi-purpose resource connecting quantification and meta-data for each protein.  ...  Dose response curves are fitted using a 4-parameterlog-logistic regression (23) .  ... 
doi:10.1093/nar/gkx1029 pmid:29106664 pmcid:PMC5753189 fatcat:iyj7fcq7uvgppb4tkgz2wpia7u

Prediction of high-responding peptides for targeted protein assays by mass spectrometry

Vincent A Fusaro, D R Mani, Jill P Mesirov, Steven A Carr
2009 Nature Biotechnology  
Identification of the most effective signature peptides, particularly in the absence of experimental data, remains a major resource constraint in developing targeted MS-based assays.  ...  proteome with a wide range of protein concentrations.  ...  We thank Rushdy Ahmad, Kathy Do, Amy Ham, Emily Rudomin, and Shao-En Ong for MS data generation, and Hasmik Keshishian and Terri Addona for generating the lists of validated MRM peptides.  ... 
doi:10.1038/nbt.1524 pmid:19169245 pmcid:PMC2753399 fatcat:xf3nb3jzzndaxjmsegcwopc5d4

Peptide Selection for Accurate Targeted Protein Quantification via a Dimethylation High-Resolution Mass Spectrum Strategy with a Peptide Release Kinetic Model

Qi Chen, Yirong Jiang, Yiping Ren, Meirong Ying, Baiyi Lu
2020 ACS Omega  
In this study, a workflow of peptide selection to determine proteotypic peptides using a dimethylation high-resolution mass spectrum strategy with a peptide release kinetic model was investigated and applied  ...  A crucial step in accurate targeted protein quantification using targeted proteomics is to determine optimal proteotypic peptides representing targeted proteins.  ...  On the basis of the peptide release kinetic model, a comprehensive workflow of peptide selection for accurate targeted protein quantification was developed using a dimethylation highresolution mass spectrum  ... 
doi:10.1021/acsomega.9b02002 pmid:32149207 pmcid:PMC7057324 fatcat:crmn7d3ixvapnesxva3qdqnf5e

PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows

Eric W Deutsch, Henry Lam, Ruedi Aebersold
2008 EMBO Reports  
This will require a new approach to proteomics that is based on emerging targeted quantitative mass spectrometry techniques.  ...  The PeptideAtlas Project comprises a growing, publicly accessible database of peptides identified in many tandem mass spectrometry proteomics studies and software tools that allow the building of PeptideAtlas  ...  For proteomics to have a key role in systems biology experimentation, it must be able to deliver accurate, absolute or relative quantification for all relevant proteins for each perturbation performed.  ... 
doi:10.1038/embor.2008.56 pmid:18451766 pmcid:PMC2373374 fatcat:4m67nc5e35azzkxlcllwqugmue

Synthetic Peptide Arrays for Pathway-Level Protein Monitoring by Liquid Chromatography-Tandem Mass Spectrometry

Johannes A. Hewel, Jian Liu, Kento Onishi, Vincent Fong, Shamanta Chandran, Jonathan B. Olsen, Oxana Pogoutse, Mike Schutkowski, Holger Wenschuh, Dirk F. H. Winkler, Larry Eckler, Peter W. Zandstra (+1 others)
2010 Molecular & Cellular Proteomics  
The method offers a flexible, rapid, and cost-effective means for routine proteomic exploration of biological systems including "label-free" quantification, while minimizing spurious interferences.  ...  Our stepwise approach consists of: (i) synthesizing microscale peptide arrays, including heavy isotope-labeled internal standards, for use as high quality references to (ii) build empirically validated  ...  We thank Thomas Kislinger and Andrei Starostin for the contribution of Orbitrap data, Pierre Havugimana for analyzing the mESC nuclear extracts using prefractionation, Carl White for feedback on the manuscript  ... 
doi:10.1074/mcp.m900456-mcp200 pmid:20467045 pmcid:PMC2984235 fatcat:zptbemhukvgvlmnuf3uvqp37dq

Liquid Chromatography-Mass Spectrometry-based Quantitative Proteomics

Fang Xie, Tao Liu, Wei-Jun Qian, Vladislav A. Petyuk, Richard D. Smith
2011 Journal of Biological Chemistry  
Fig. 1 illustrates an LC-MS-based global proteomic workflow in which proteins are converted into peptides for identification and quantification (i.e. "bottom-up" proteomics).  ...  Challenges affecting quantification in a bottom-up proteomic workflow stem from the wide range of peptide and protein physicochemical properties that give rise to large differences in MS responses (8).  ...  Peptides are identified by matching accurate mass and normalized elution time features to those stored in a previously established reference database of peptides.  ... 
doi:10.1074/jbc.r110.199703 pmid:21632532 pmcid:PMC3138289 fatcat:i6u7yfdugbfwdeycakftmizw6e

Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification

Chad R. Weisbrod, Jimmy K. Eng, Michael R. Hoopmann, Tahmina Baker, James E. Bruce
2012 Journal of Proteome Research  
FT All Reaction Monitoring (FT-ARM) is a novel approach for the identification and quantification of peptides that relies upon the selectivity of high mass accuracy data and the specificity of peptide  ...  A dot product score is calculated against each spectrum in order to generate a score chromatogram used for both identification and quantification.  ...  Priska D. von Haller for helpful discussion. Bibliography  ... 
doi:10.1021/pr2008175 pmid:22288382 pmcid:PMC3319072 fatcat:k54ofu734rhzvpu6ijyl5jjpiu

Recent developments in quantitative proteomics

Christopher H. Becker, Marshall Bern
2011 Mutation Research. Genetic Toxicology and Environmental Mutagenesis  
This review article then includes a short discussion of LC-MS approaches to three-dimensional structure determination and concludes with a section on statistics and data mining for proteomics, including  ...  Then a discussion follows on the various computational techniques used to identify peptides and proteins from LC-MS/MS data.  ...  Mass spectrometry for 3D structure Some experimental techniques based on mass spectrometry can give structural information about biological molecules and complexes [5] .  ... 
doi:10.1016/j.mrgentox.2010.06.016 pmid:20620221 pmcid:PMC2980806 fatcat:42hsowazinhb5ib3uo6h25qfqu

Increased Selectivity, Analytical Precision, and Throughput in Targeted Proteomics

Reiko Kiyonami, Alan Schoen, Amol Prakash, Scott Peterman, Vlad Zabrouskov, Paola Picotti, Ruedi Aebersold, Andreas Huhmer, Bruno Domon
2010 Molecular & Cellular Proteomics  
The technique is integrated into a linear workflow including experimental design, data acquisition, and data evaluation enabling large scale proteomic studies.  ...  Mass spectrometry LC-MS experiments were performed on a triple quadrupole mass spectrometer (TSQ Vantage, Thermo Scientific) operated in the nano-electrospray mode.  ...  Response curves for all eight spiked isotopically labeled peptides cover a wide dynamic range using the iSRM method.  ... 
doi:10.1074/mcp.m110.002931 pmid:20664071 pmcid:PMC3033677 fatcat:mst2vps4hncbtdukrliqu7a2lq

Quantitative Mass Spectrometry-based Proteomics Reveals the Dynamic Range of Primary Mouse Astrocyte Protein Secretion

Todd M. Greco, Steven H. Seeholzer, Adrian Mak, Lynn Spruce, Harry Ischiropoulos
2010 Journal of Proteome Research  
The current work utilized SILAC-generated isotope reference proteomes to quantify relative protein abundances between the astrocyte proteome and secretome.  ...  Growing appreciation for astrocytes as active participants in nervous system development, neurovascular metabolic coupling, and neurological disease progression has stimulated recent investigation into  ...  Acknowledgments We thank Jessica Lee in the CHOP Protein Core for her assistance in operating and maintaining the mass spectrometers.  ... 
doi:10.1021/pr100134n pmid:20329800 pmcid:PMC2866110 fatcat:va24cmwfzbaddbslfxk6gsfwkq

Detection of co-eluted peptides using database search methods

Gelio Alves, Aleksey Y Ogurtsov, Siwei Kwok, Wells W Wu, Guanghui Wang, Rong-Fong Shen, Yi-Kuo Yu
2008 Biology Direct  
Current experimental techniques, especially those applying liquid chromatography mass spectrometry, have made high-throughput proteomic studies possible.  ...  The increase in throughput however also raises concerns on the accuracy of identification or quantification.  ...  Based on our theoretical analysis (see Figure 1 ), peptides will be co-eluted all the time during a large scale HPLC/MS proteomics experiment.  ... 
doi:10.1186/1745-6150-3-27 pmid:18597684 pmcid:PMC2483259 fatcat:mitcaqcptvgx7cqnk2xqu4ceey

Novel alternative splicing isoform biomarkers identification from high-throughput plasma proteomics profiling of breast cancer

Fan Zhang, Mu Wang, Tran Michael, Renee Drabier
2013 BMC Systems Biology  
Conclusions: We developed a peptidomics approach for the proteomics community to analyze, identify, and characterize alternative splicing isoforms from MS-based proteomics experiments with more coverage  ...  Results: Therefore, we presented a peptidomics approach to searching novel alternative splicing isoforms in clinical proteomics.  ...  The proteomics study for biomarker discovery was supported by the National Cancer Institute Clinical Proteomics Technology Assessment for Cancer program (U24 CA126480).  ... 
doi:10.1186/1752-0509-7-s5-s8 pmid:24565027 pmcid:PMC4028860 fatcat:eyi7zdlvqrg7diaipmcbvlklty

Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0

Paulo C Carvalho, Diogo B Lima, Felipe V Leprevost, Marlon D M Santos, Juliana S G Fischer, Priscila F Aquino, James J Moresco, John R Yates, Valmir C Barbosa
2015 Nature Protocols  
of data with regard to the Gene ontology database. the patternlab for proteomics 4.0 package brings together all of these modules in a self-contained software environment, which allows for complete proteomic  ...  of sequence databases, peptide spectrum matching, statistical filtering and data organization, extracting quantitative information from label-free and chemically labeled data, and analyzing statistics  ...  When searching for peptide candidates within a database, a precursor mass tolerance must be specified.  ... 
doi:10.1038/nprot.2015.133 pmid:26658470 pmcid:PMC5722229 fatcat:hgi75jg6ybcfdcp4zmtr75wdqy

New Strategies and Challenges in Lung Proteomics and Metabolomics. An Official American Thoracic Society Workshop Report

Russell P. Bowler, Chris H. Wendt, Michael B. Fessler, Matthew W. Foster, Rachel S. Kelly, Jessica Lasky-Su, Angela J. Rogers, Kathleen A. Stringer, Brent W. Winston
2017 Annals of the American Thoracic Society  
on the lung; (4) integrative platforms across genetic and genomic databases that can be applied to lung-related metabolomic and proteomic studies; and (5) the clinical applications of proteomics and metabolomics  ...  and challenges of lung-specific biological specimens for metabolomic and proteomic analysis; (3) the diverse informatics approaches and databases unique to metabolomics and proteomics, with special emphasis  ...  Special thanks to Aubrey Shoe, National Jewish Health, for administrative assistance, and ATS administrative staff Breana Portelli and Kimberly Lawrence.  ... 
doi:10.1513/annalsats.201710-770ws pmid:29192815 pmcid:PMC5946579 fatcat:pjzokf6ej5dlfdxfzztttunnca
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