Crux: Rapid Open Source Protein Tandem Mass Spectrometry Analysis

Efficiently and accurately analyzing big protein tandem mass spectrometry data sets requires robust software that incorporates state-of-the-art computational, machine learning, and statistical methods. The Crux mass spectrometry analysis software toolkit (http://cruxtoolkit.sourceforge.net) is an open source project that aims to provide users with a cross-platform suite of analysis tools for interpreting protein mass spectrometry data.

[1]  William Stafford Noble,et al.  Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data. , 2010, Journal of proteome research.

[2]  Jerry D. Holman,et al.  Identifying Proteomic LC‐MS/MS Data Sets with Bumbershoot and IDPicker , 2012, Current protocols in bioinformatics.

[3]  Michael J MacCoss,et al.  Comparison of database search strategies for high precursor mass accuracy MS/MS data. , 2010, Journal of proteome research.

[4]  J. Eng,et al.  Comet: An open‐source MS/MS sequence database search tool , 2013, Proteomics.

[5]  Benjamin Thomas,et al.  CPFP: a central proteomics facilities pipeline , 2010, Bioinform..

[6]  William Stafford Noble,et al.  Faster SEQUEST searching for peptide identification from tandem mass spectra. , 2011, Journal of proteome research.

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

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

[9]  Dan Xie,et al.  Variation and Genetic Control of Protein Abundance in Humans , 2013, Nature.

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

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

[12]  William Stafford Noble,et al.  Direct Maximization of Protein Identifications from Tandem Mass Spectra* , 2011, Molecular & Cellular Proteomics.

[13]  William Stafford Noble,et al.  Detecting cross-linked peptides by searching against a database of cross-linked peptide pairs. , 2010, Journal of proteome research.

[14]  Wen Gao,et al.  pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry , 2005, Bioinform..

[15]  M. Mann,et al.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.

[16]  J. Yates,et al.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database , 1994, Journal of the American Society for Mass Spectrometry.

[17]  Natalie I. Tasman,et al.  A guided tour of the Trans‐Proteomic Pipeline , 2010, Proteomics.

[18]  Michael Riffle,et al.  A Mass Spectrometry Proteomics Data Management Platform* , 2012, Molecular & Cellular Proteomics.

[19]  William Stafford Noble,et al.  Estimating relative abundances of proteins from shotgun proteomics data , 2012, BMC Bioinformatics.

[20]  Edward L Huttlin,et al.  Global analysis of protein expression and phosphorylation of three stages of Plasmodium falciparum intraerythrocytic development. , 2013, Journal of proteome research.

[21]  William Stafford Noble,et al.  Computing Exact p-values for a Cross-correlation Shotgun Proteomics Score Function , 2014, Molecular & Cellular Proteomics.

[22]  William Stafford Noble,et al.  Semi-supervised learning for peptide identification from shotgun proteomics datasets , 2007, Nature Methods.