title: MSAcquisitionSimulator: data-dependent acquisition simulator for LC-MS shotgun proteomics.
abstract: Data-dependent acquisition (DDA) is the most common method used to control the acquisition process of shotgun proteomics experiments. While novel DDA approaches have been proposed, their evaluation is made difficult by the need of programmatic control of a mass spectrometer. An alternative is in silico analysis, for which suitable software has been unavailable. To meet this need, we have developed MSAcquisitionSimulator-a collection of C ++ programs for simulating ground truth LC-MS data and the subsequent application of custom DDA algorithms. It provides an opportunity for researchers to test, refine and evaluate novel DDA algorithms prior to implementation on a mass spectrometer.
  
  
  
  The software is freely available from its Github repository http://www.github.com/DennisGoldfarb/MSAcquisitionSimulator/ which contains further documentation and usage instructions.
  
  
  
  weiwang@cs.ucla.edu or ben_major@med.unc.edu
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
authors.forename: Dennis
authors.initials: D
authors.lastname: Goldfarb
authors.affiliation: Department of Computer Science, University of California, Los Angeles, CA, USA and.
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
authors.affiliation: Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA, Department of Cell Biology and Physiology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
authors.forename: Michael B
authors.initials: MB
authors.lastname: Major
mesh_terms: D000465:Algorithms; D002853:Chromatography, Liquid / Q000379:methods*; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D040901:Proteomics / Q000379:methods*; D012984:Software