metrics from mass spectrometry experiments

[1]  Lennart Martens,et al.  The PSI semantic validator: A framework to check MIAPE compliance of proteomics data , 2009, Proteomics.

[2]  Henning Hermjakob,et al.  Ten Years of Standardizing Proteomic Data: A Report on the HUPO‐PSI Spring Workshop , 2012, Proteomics.

[3]  Lennart Martens,et al.  Quality Control in Proteomics , 2011, Proteomics.

[4]  Lennart Martens,et al.  Bringing proteomics into the clinic: The need for the field to finally take itself seriously , 2013, Proteomics. Clinical applications.

[5]  Martin Eisenacher,et al.  Controlled vocabularies and ontologies in proteomics: Overview, principles and practice , 2014, Biochimica et biophysica acta.

[6]  Lennart Martens,et al.  ms_lims, a simple yet powerful open source laboratory information management system for MS‐driven proteomics , 2010, Proteomics.

[7]  David L Tabb,et al.  Quality assessment for clinical proteomics. , 2013, Clinical biochemistry.

[8]  John T. Prince,et al.  Metriculator: quality assessment for mass spectrometry-based proteomics , 2013, Bioinform..

[9]  I. Eidhammer,et al.  Improving the reliability and throughput of mass spectrometry‐based proteomics by spectrum quality filtering , 2006, Proteomics.

[10]  Paul N. Schofield,et al.  The Units Ontology: a tool for integrating units of measurement in science , 2012, Database J. Biol. Databases Curation.

[11]  David L. Tabb,et al.  Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses* , 2009, Molecular & Cellular Proteomics.

[12]  Lennart Martens,et al.  mzML—a Community Standard for Mass Spectrometry Data* , 2010, Molecular & Cellular Proteomics.

[13]  Fredrik Levander,et al.  Data processing methods and quality control strategies for label-free LC-MS protein quantification. , 2014, Biochimica et biophysica acta.

[14]  Robert E. Kearney,et al.  A HUPO test sample study reveals common problems in mass spectrometry-based proteomics , 2009, Nature Methods.

[15]  K. Gevaert,et al.  Improved recovery of proteome‐informative, protein N‐terminal peptides by combined fractional diagonal chromatography (COFRADIC) , 2008, Proteomics.

[16]  Lennart Martens,et al.  TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists* , 2011, Molecular & Cellular Proteomics.

[17]  Xu Shi,et al.  Performance characteristics of an FT MS‐based workflow for label‐free differential MS analysis of human plasma: standards, reproducibility, targeted feature investigation, and application to a model of controlled myocardial infarction , 2008, Proteomics. Clinical applications.

[18]  Karl Mechtler,et al.  Interlaboratory studies and initiatives developing standards for proteomics , 2013, Proteomics.

[19]  Knut Reinert,et al.  TOPP - the OpenMS proteomics pipeline , 2007, Bioinform..

[20]  Martin Eisenacher,et al.  The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results , 2012, Molecular & Cellular Proteomics.

[21]  Jens Krüger,et al.  From the Desktop to the Grid: conversion of KNIME Workflows to gUSE , 2013, IWSG.

[22]  Martin Eisenacher,et al.  The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary , 2013, Database J. Biol. Databases Curation.

[23]  Lorenzo J. Vega-Montoto,et al.  QuaMeter: multivendor performance metrics for LC-MS/MS proteomics instrumentation. , 2012, Analytical chemistry.

[24]  Robertson Craig,et al.  TANDEM: matching proteins with tandem mass spectra. , 2004, Bioinformatics.

[25]  Martin Eisenacher,et al.  Using Laboratory Information Management Systems as central part of a proteomics data workflow , 2010, Proteomics.

[26]  Fredrik Levander,et al.  Automated quality control system for LC-SRM setups. , 2013, Journal of proteomics.

[27]  Thorsten Meinl,et al.  KNIME: The Konstanz Information Miner , 2007, GfKl.

[28]  Lennart Martens,et al.  A posteriori quality control for the curation and reuse of public proteomics data , 2011, Proteomics.

[29]  M. Ashburner,et al.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration , 2007, Nature Biotechnology.

[30]  Knut Reinert,et al.  OpenMS – An open-source software framework for mass spectrometry , 2008, BMC Bioinformatics.

[31]  Michel Schneider,et al.  UniProtKB/Swiss-Prot. , 2007, Methods in molecular biology.

[32]  Lennart Martens,et al.  The Ontology Lookup Service: bigger and better , 2010, Nucleic Acids Res..

[33]  Karl Mechtler,et al.  SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC–MS Performance Metrics on Orbitrap Instruments , 2012, Journal of proteome research.