title: Estimating relative abundances of proteins from shotgun proteomics data.
abstract: BACKGROUND
  Spectral counting methods provide an easy means of identifying proteins with differing abundances between complex mixtures using shotgun proteomics data. The crux spectral-counts command, implemented as part of the Crux software toolkit, implements four previously reported spectral counting methods, the spectral index (SI(N)), the exponentially modified protein abundance index (emPAI), the normalized spectral abundance factor (NSAF), and the distributed normalized spectral abundance factor (dNSAF).
  
  
  RESULTS
  We compared the reproducibility and the linearity relative to each protein's abundance of the four spectral counting metrics. Our analysis suggests that NSAF yields the most reproducible counts across technical and biological replicates, and both SI(N) and NSAF achieve the best linearity.
  
  
  CONCLUSIONS
  With the crux spectral-counts command, Crux provides open-source modular methods to analyze mass spectrometry data for identifying and now quantifying peptides and proteins. The C++ source code, compiled binaries, spectra and sequence databases are available at http://noble.gs.washington.edu/proj/crux-spectral-counts.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA, USA.
authors.forename: Sean
authors.initials: S
authors.lastname: McIlwain
authors.forename: Michael
authors.initials: M
authors.lastname: Mathews
authors.forename: Michael S
authors.initials: MS
authors.lastname: Bereman
authors.forename: Edwin W
authors.initials: EW
authors.lastname: Rubel
authors.forename: Michael J
authors.initials: MJ
authors.lastname: MacCoss
authors.forename: William Stafford
authors.initials: WS
authors.lastname: Noble
mesh_terms: D013058:Mass Spectrometry; D010455:Peptides / Q000032:analysis; D011506:Proteins / Q000032:analysis* / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods
chemical_list: D010455:Peptides; D011506:Proteins