Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles).
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Richard D Smith | Mark Baker | John R Yates | Henning Hermjakob | Hans-Joachim Kraus | Christoph H Borchers | Akhilesh Pandey | Peipei Ping | Patrik Kolar | Christopher R Kinsinger | Henry Rodriguez | Eric W Deutsch | Rune Linding | David L Tabb | Gilbert S Omenn | David Horn | James Apffel | Xiaopeng Bian | Ralph Bradshaw | Mi-Youn Brusniak | Daniel W Chan | Bruno Domon | Jeff Gorman | Rudolf Grimm | William Hancock | Christie Hunter | Hanno Langen | Robert L Moritz | Ron Orlando | Amir Rahbar | Robert Rivers | Sean L Seymour | Richard J Simpson | Douglas Slotta | Stephen E Stein | Danilo Tagle | Richard D. Smith | J. Yates | R. Moritz | G. Omenn | H. Hermjakob | E. Deutsch | R. Linding | P. Ping | M. Brusniak | D. Tabb | C. Borchers | W. Hancock | B. Domon | R. Simpson | H. Rodriguez | M. Baker | S. Stein | D. Slotta | C. Kinsinger | S. Seymour | Patrik Kolar | H. Langen | Hans-Joachim Kraus | R. Orlando | R. Grimm | Robert C. Rivers | A. Rahbar | C. Hunter | J. Apffel | Ralph Bradshaw | David Horn | Danilo A. Tagle | Xiaopeng Bian | J. Gorman | D. Chan | A. Pandey
[1] Mehdi Mesri,et al. Evolution of clinical proteomics and its role in medicine. , 2011, Journal of proteome research.
[2] Pierre Baldi,et al. The Stability and Complexity of Antibody Responses to the Major Surface Antigen of Plasmodium falciparum Are Associated with Age in a Malaria Endemic Area* , 2011, Molecular & Cellular Proteomics.
[3] Birgit Schilling,et al. Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. , 2010, Journal of proteome research.
[4] C. Turck,et al. The Association of Biomolecular Resource Facilities Proteomics Research Group 2006 Study , 2007, Molecular & Cellular Proteomics.
[5] Alexey I Nesvizhskii,et al. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. , 2002, Analytical chemistry.
[6] Birgit Schilling,et al. Interlaboratory Study Characterizing a Yeast Performance Standard for Benchmarking LC-MS Platform Performance* , 2009, Molecular & Cellular Proteomics.
[7] William Stafford Noble,et al. Statistical calibration of the SEQUEST XCorr function. , 2009, Journal of proteome research.
[8] S. Carr,et al. Reporting Protein Identification Data , 2006, Molecular & Cellular Proteomics.
[9] Martin Eisenacher,et al. Implementing Data Standards: A report on the HUPOPSI Workshop September 2009, Toronto, Canada , 2010, Proteomics.
[10] Jason E. Stewart,et al. Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.
[11] Michael D. Litton,et al. IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering. , 2009, Journal of proteome research.
[12] John R Yates,et al. Colander: a probability-based support vector machine algorithm for automatic screening for CID spectra of phosphopeptides prior to database search. , 2008, Journal of proteome research.
[13] Robertson Craig,et al. Open source system for analyzing, validating, and storing protein identification data. , 2004, Journal of proteome research.
[14] Maureen Kachman,et al. Validated MALDI-TOF/TOF mass spectra for protein standards , 2007, Journal of the American Society for Mass Spectrometry.
[15] J. Yates,et al. DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. , 2002, Journal of proteome research.
[16] R. Aebersold,et al. mProphet: automated data processing and statistical validation for large-scale SRM experiments , 2011, Nature Methods.
[17] Ruedi Aebersold,et al. The Need for Guidelines in Publication of Peptide and Protein Identification Data , 2004, Molecular & Cellular Proteomics.
[18] David L. Tabb,et al. Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses* , 2009, Molecular & Cellular Proteomics.
[19] James A Hill,et al. Proteomics FASTA Archive and Reference Resource , 2008, Proteomics.
[20] Christoph H Borchers,et al. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma , 2009, Nature Biotechnology.
[21] Lennart Martens,et al. mzML—a Community Standard for Mass Spectrometry Data* , 2010, Molecular & Cellular Proteomics.
[22] William Stafford Noble,et al. Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. , 2008, Journal of proteome research.
[23] Ralph A Bradshaw. Revised draft guidelines for proteomic data publication. , 2005, Molecular & cellular proteomics : MCP.
[24] J. Yates,et al. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. , 2004, Analytical chemistry.
[25] Bingwen Lu,et al. Automatic validation of phosphopeptide identifications from tandem mass spectra. , 2007, Analytical chemistry.
[26] Phil Andrews,et al. Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. , 2009, Journal of proteome research.
[27] Lennart Martens,et al. The minimum information about a proteomics experiment (MIAPE) , 2007, Nature Biotechnology.
[28] Cathy H. Wu,et al. The Human Proteome Project: Current State and Future Direction , 2011, Molecular & Cellular Proteomics.
[29] John R. Yates,et al. Census for Proteome Quantification , 2010, Current protocols in bioinformatics.
[30] James A Hill,et al. ProteomeCommons.org collaborative annotation and project management resource integrated with the Tranche repository. , 2010, Journal of proteome research.
[31] Heidi Zhang,et al. Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer. , 2007, Journal of proteome research.
[32] Ruedi Aebersold,et al. The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools. , 2008, Journal of proteome research.
[33] R. Aebersold,et al. A statistical model for identifying proteins by tandem mass spectrometry. , 2003, Analytical chemistry.
[34] William Stafford Noble,et al. Semi-supervised learning for peptide identification from shotgun proteomics datasets , 2007, Nature Methods.
[35] Ruedi Aebersold,et al. High-throughput generation of selected reaction-monitoring assays for proteins and proteomes , 2010, Nature Methods.
[36] Susan E Abbatiello,et al. Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry. , 2010, Clinical chemistry.
[37] E. Deutsch. mzML: A single, unifying data format for mass spectrometer output , 2008, Proteomics.
[38] Henry H. N. Lam,et al. PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows , 2008, EMBO reports.
[39] Jayson A. Falkner,et al. Tranche: decentralized data storage for the proteomics community , 2007 .
[40] Steven A. Carr,et al. New Guidelines for Clinical Proteomics Manuscripts , 2008, Molecular & Cellular Proteomics.
[41] R. Appel,et al. Guidelines for the next 10 years of proteomics , 2009, Proteomics.
[42] R. Aebersold,et al. A High-Confidence Human Plasma Proteome Reference Set with Estimated Concentrations in PeptideAtlas* , 2011, Molecular & Cellular Proteomics.
[43] Lennart Martens,et al. The Proteomics Identifications database: 2010 update , 2009, Nucleic Acids Res..
[44] R. Aebersold,et al. Dynamic Spectrum Quality Assessment and Iterative Computational Analysis of Shotgun Proteomic Data , 2006, Molecular & Cellular Proteomics.
[45] Rolf Apweiler,et al. The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible , 2006, Expert review of proteomics.
[46] K. Parker,et al. Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents*S , 2004, Molecular & Cellular Proteomics.
[47] Gilbert S Omenn,et al. The Human Proteome Organization Plasma Proteome Project pilot phase: Reference specimens, technology platform comparisons, and standardized data submissions and analyses , 2004, Proteomics.