Public proteomics data: How the field has evolved from sceptical inquiry to the promise of in silico proteomics☆

Graphical abstract

[1]  Ron Edgar,et al.  NCBI Peptidome: a new public repository for mass spectrometry peptide identifications , 2009, Nature Biotechnology.

[2]  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.

[3]  P ? ? ? ? ? ? ? % ? ? ? ? , 1991 .

[4]  Knut Reinert,et al.  Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry , 2015, Proteomics.

[5]  S. Bryant,et al.  Open mass spectrometry search algorithm. , 2004, Journal of proteome research.

[6]  Lennart Martens,et al.  jqcML: an open-source java API for mass spectrometry quality control data in the qcML format. , 2014, Journal of proteome research.

[7]  Juan Antonio Vizcaíno,et al.  Introducing the PRIDE Archive RESTful web services , 2015, Nucleic Acids Res..

[8]  James A Hill,et al.  Proteomics FASTA Archive and Reference Resource , 2008, Proteomics.

[9]  Lennart Martens,et al.  Pladipus Enables Universal Distributed Computing in Proteomics Bioinformatics. , 2016, Journal of proteome research.

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

[11]  Lennart Martens Resilience in the proteomics data ecosystem: How the field cares for its data , 2013, Proteomics.

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

[13]  Juan Antonio Vizcaíno,et al.  From Peptidome to PRIDE: Public proteomics data migration at a large scale , 2013, Proteomics.

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

[15]  Rong Wang,et al.  The need for a public proteomics repository , 2004, Nature Biotechnology.

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

[17]  Johannes Griss,et al.  PRIDE Cluster: building a consensus of proteomics data , 2013, Nature Methods.

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

[19]  Lennart Martens A report on the ESF workshop on quality control in proteomics. , 2010, Molecular bioSystems.

[20]  Lennart Martens,et al.  PRIDE: The proteomics identifications database , 2005, Proteomics.

[21]  Andrew R. Jones,et al.  ProteomeXchange provides globally co-ordinated proteomics data submission and dissemination , 2014, Nature Biotechnology.

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

[23]  Lennart Martens,et al.  PRIDE Converter: making proteomics data-sharing easy , 2009, Nature Biotechnology.

[24]  Robertson Craig,et al.  Open source system for analyzing, validating, and storing protein identification data. , 2004, Journal of proteome research.

[25]  Lennart Martens,et al.  iMonDB: Mass Spectrometry Quality Control through Instrument Monitoring. , 2015, Journal of proteome research.

[26]  Lennart Martens,et al.  PRIDE Inspector: a tool to visualize and validate MS proteomics data , 2011, Nature Biotechnology.

[27]  Lennart Martens,et al.  LNCipedia: a database for annotated human lncRNA transcript sequences and structures , 2012, Nucleic Acids Res..

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

[29]  J. Vandesompele,et al.  An update on LNCipedia: a database for annotated human lncRNA sequences , 2015, Nucleic Acids Res..

[30]  L. Martens,et al.  Ten years of public proteomics data: How things have evolved, and where the next ten years should lead us , 2015 .

[31]  R. Aebersold,et al.  Mass spectrometry-based proteomics , 2003, Nature.

[32]  J. Yates,et al.  Probability-based validation of protein identifications using a modified SEQUEST algorithm. , 2002, Analytical chemistry.

[33]  Lennart Martens,et al.  A la carte proteomics with an emphasis on gel‐free techniques , 2007, Proteomics.

[34]  Lennart Martens,et al.  The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium , 2012, Molecular & Cellular Proteomics.

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

[36]  Lennart Martens,et al.  Crowdsourcing in proteomics: public resources lead to better experiments , 2013, Amino Acids.

[37]  Michael J Sweredoski,et al.  LogViewer: a software tool to visualize quality control parameters to optimize proteomics experiments using Orbitrap and LTQ-FT mass spectrometers. , 2011, Journal of biomolecular techniques : JBT.

[38]  Lennart Martens,et al.  Pride-asap: Automatic fragment ion annotation of identified PRIDE spectra☆ , 2013, Journal of proteomics.

[39]  Joshua E. Elias,et al.  Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. , 2003, Journal of proteome research.

[40]  Wei Sun,et al.  RScore: a peptide randomicity score for evaluating tandem mass spectra. , 2004, Rapid communications in mass spectrometry : RCM.

[41]  Nichole L. King,et al.  Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry , 2004, Genome Biology.

[42]  Eystein Oveland,et al.  PeptideShaker enables reanalysis of MS-derived proteomics data sets , 2015, Nature Biotechnology.

[43]  R. Beavis,et al.  Using annotated peptide mass spectrum libraries for protein identification. , 2006, Journal of proteome research.

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

[45]  Lennart Martens,et al.  Current methods for global proteome identification , 2012, Expert review of proteomics.

[46]  Lennart Martens,et al.  The minimum information about a proteomics experiment (MIAPE) , 2007, Nature Biotechnology.

[47]  Lennart Martens,et al.  sORFs.org: a repository of small ORFs identified by ribosome profiling , 2015, Nucleic Acids Res..

[48]  Robertson Craig,et al.  The use of proteotypic peptide libraries for protein identification. , 2005, Rapid communications in mass spectrometry : RCM.

[49]  Lennart Martens,et al.  Proteomics data repositories: Providing a safe haven for your data and acting as a springboard for further research , 2010, Journal of proteomics.

[50]  J. Vizcaíno,et al.  Exploring the potential of public proteomics data , 2015, Proteomics.

[51]  Lennart Martens,et al.  qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments , 2014, Molecular & Cellular Proteomics.

[52]  Martin Eisenacher,et al.  The mzQuantML Data Standard for Mass Spectrometry–based Quantitative Studies in Proteomics , 2013, Molecular & Cellular Proteomics.

[53]  Rui Wang,et al.  PRIDE: Quality control in a proteomics data repository , 2012, Database J. Biol. Databases Curation.