mspire: mass spectrometry proteomics in Ruby
Open Access
- 16 October 2008
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 24 (23), 2796-2797
- https://doi.org/10.1093/bioinformatics/btn513
Abstract
Summary: Mass spectrometry-based proteomics stands to gain from additional analysis of its data, but its large, complex datasets make demands on speed and memory usage requiring special consideration from scripting languages. The software library ‘mspire’—developed in the Ruby programming language—offers quick and memory-efficient readers for standard xml proteomics formats, converters for intermediate file types in typical proteomics spectral-identification work flows (including the Bioworks .srf format), and modules for the calculation of peptide false identification rates. Availability: Freely available at http://mspire.rubyforge.org. Additional data models, usage information, and methods available at http://bioinformatics.icmb.utexas.edu/mspire Contact: marcotte@icmb.utexas.eduKeywords
This publication has 4 references indexed in Scilit:
- Semi-supervised learning for peptide identification from shotgun proteomics datasetsNature Methods, 2007
- ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formatsBioinformatics, 2006
- InSilicoSpectro: An Open-Source Proteomics LibraryJournal of Proteome Research, 2006
- The PeptideAtlas projectNucleic Acids Research, 2006