Supporting Advances in Proteome Informatics*□S

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[1]  K. Reinert,et al.  OpenMS: a flexible open-source software platform for mass spectrometry data analysis , 2016, Nature Methods.

[2]  R. Aebersold,et al.  Crosslinking and Mass Spectrometry: An Integrated Technology to Understand the Structure and Function of Molecular Machines. , 2016, Trends in biochemical sciences.

[3]  Martin Eisenacher,et al.  PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets , 2015, Molecular & Cellular Proteomics.

[4]  Helmut E Meyer,et al.  ProCon - PROteomics CONversion tool. , 2015, Journal of proteomics.

[5]  Oliver Brock,et al.  Serum Albumin Domain Structures in Human Blood Serum by Mass Spectrometry and Computational Biology , 2015, Molecular & Cellular Proteomics.

[6]  Haruki Nakamura,et al.  Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. , 2015, Structure.

[7]  Martin Eisenacher,et al.  PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface. , 2015, Journal of proteome research.

[8]  Fredrik Levander,et al.  Representation of selected-reaction monitoring data in the mzQuantML data standard , 2015, Proteomics.

[9]  Juan Antonio Vizcaíno,et al.  ms-data-core-api: an open-source, metadata-oriented library for computational proteomics , 2015, Bioinform..

[10]  Martin Eisenacher,et al.  Development of data representation standards by the human proteome organization proteomics standards initiative , 2015, J. Am. Medical Informatics Assoc..

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

[12]  Andrew R Jones,et al.  ProteoAnnotator – Open source proteogenomics annotation software supporting PSI standards , 2014, Proteomics.

[13]  Martin Eisenacher,et al.  A standardized framing for reporting protein identifications in mzIdentML 1.2 , 2014, Proteomics.

[14]  A. Nesvizhskii.  Proteogenomics: concepts, applications and computational strategies , 2014, Nature Methods.

[15]  Pavel A. Pevzner,et al.  Universal database search tool for proteomics , 2014, Nature Communications.

[16]  Juan Antonio Vizcaíno,et al.  How to submit MS proteomics data to ProteomeXchange via the PRIDE database , 2014, Proteomics.

[17]  Jun Fan,et al.  The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience* , 2014, Molecular & Cellular Proteomics.

[18]  Robert J. Chalkley,et al.  Matching Cross-linked Peptide Spectra: Only as Good as the Worse Identification* , 2013, Molecular & Cellular Proteomics.

[19]  Juan Antonio Vizcaíno,et al.  Tools (Viewer, Library and Validator) that Facilitate Use of the Peptide and Protein Identification Standard Format, Termed mzIdentML , 2013, Molecular & Cellular Proteomics.

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

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

[22]  Natalie I. Tasman,et al.  A Cross-platform Toolkit for Mass Spectrometry and Proteomics , 2012, Nature Biotechnology.

[23]  Juan Antonio Vizcaíno,et al.  jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data , 2012, Proteomics.

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

[25]  K. Clauser,et al.  Modification Site Localization Scoring: Strategies and Performance , 2012, Molecular & Cellular Proteomics.

[26]  Bin Ma,et al.  PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification* , 2011, Molecular & Cellular Proteomics.

[27]  Natalie I. Tasman,et al.  iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates* , 2011, Molecular & Cellular Proteomics.

[28]  Ville R. Koskinen,et al.  Hierarchical Clustering of Shotgun Proteomics Data , 2011, Molecular & Cellular Proteomics.

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

[30]  B. Searle.  Scaffold: A bioinformatic tool for validating MS/MS‐based proteomic studies , 2010, Proteomics.

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

[32]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[33]  Norman W. Paton,et al.  Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines , 2009, Proteomics.

[34]  William Stafford Noble,et al.  Rapid and accurate peptide identification from tandem mass spectra. , 2008, Journal of proteome research.

[35]  B. Searle,et al.  Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies. , 2008, Journal of proteome research.

[36]  Lennart Martens,et al.  The PSI formal document process and its implementation on the PSI website , 2007, Proteomics.

[37]  D. Tabb,et al.  MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. , 2007, Journal of proteome research.

[38]  M. Mann,et al.  What does it mean to identify a protein in proteomics? , 2002, Trends in biochemical sciences.