Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)

The Human Proteome Project: Current State and Future Direction

(2011) Pierre Legrain et al.   MOLECULAR & CELLULAR PROTEOMICS

mProphet: automated data processing and statistical validation for large-scale SRM experiments

(2011) Lukas Reiter et al.   NATURE METHODS

ProteomeCommons.org Collaborative Annotation and Project Management Resource Integrated With the Tranche Repository

(2010) James A. Hill et al.   JOURNAL OF PROTEOME RESEARCH

Evolution of Clinical Proteomics and its Role in Medicine

(2010) Emily Boja et al.   JOURNAL OF PROTEOME RESEARCH

mzML—a Community Standard for Mass Spectrometry Data

(2010) Lennart Martens et al.   MOLECULAR & CELLULAR PROTEOMICS

Implementing Data Standards: A report on the HUPOPSI Workshop September 2009, Toronto, Canada

(2010) Sandra Orchard et al.   PROTEOMICS

Automated Detection of Inaccurate and Imprecise Transitions in Peptide Quantification by Multiple Reaction Monitoring Mass Spectrometry

(2009) S. E. Abbatiello et al.   CLINICAL CHEMISTRY

Statistical Calibration of the SEQUEST XCorr Function

(2009) Aaron A. Klammer et al.   JOURNAL OF PROTEOME RESEARCH

Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: The Amsterdam Principles

(2009) Henry Rodriguez et al.   JOURNAL OF PROTEOME RESEARCH

IDPicker 2.0: Improved Protein Assembly with High Discrimination Peptide Identification Filtering

(2009) Ze-Qiang Ma et al.   JOURNAL OF PROTEOME RESEARCH

Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography−Tandem Mass Spectrometry

(2009) David L. Tabb et al.   JOURNAL OF PROTEOME RESEARCH

Interlaboratory Study Characterizing a Yeast Performance Standard for Benchmarking LC-MS Platform Performance

(2009) Amanda G. Paulovich et al.   MOLECULAR & CELLULAR PROTEOMICS

Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses

(2009) Paul A. Rudnick et al.   MOLECULAR & CELLULAR PROTEOMICS

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma

(2009) Terri A Addona et al.   NATURE BIOTECHNOLOGY

High-throughput generation of selected reaction-monitoring assays for proteins and proteomes

(2009) Paola Picotti et al.   NATURE METHODS

The Proteomics Identifications database: 2010 update

(2009) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

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

(2008) Eric W Deutsch et al.   EMBO REPORTS

Colander: A Probability-Based Support Vector Machine Algorithm for Automatic Screening for CID Spectra of Phosphopeptides Prior to Database Search

(2008) Bingwen Lu et al.   JOURNAL OF PROTEOME RESEARCH

New Guidelines for Clinical Proteomics Manuscripts

(2008) Julio E. Celis et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteomics FASTA Archive and Reference Resource

(2008) Jayson A. Falkner et al.   PROTEOMICS

mzML: A single, unifying data format for mass spectrometer output

(2008) Eric Deutsch   PROTEOMICS

The Standard Protein Mix Database: A Diverse Data Set To Assist in the Production of Improved Peptide and Protein Identification Software Tools

(2007) John Klimek et al.   JOURNAL OF PROTEOME RESEARCH

Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases

(2007) Lukas Käll et al.   JOURNAL OF PROTEOME RESEARCH