title: Speeding up tandem mass spectral identification using indexes.
abstract: BACKGROUND
  Tandem mass spectrometry (MS/MS) has been routinely used in proteomics studies. Post-translational modification (PTM) identification is a challenging problem in tandem mass spectral analysis.
  
  
  RESULTS
  In this article, we define two scoring functions for identifying peptides/proteins with PTMs from MS/MS spectra: match scores and diagonal scores, as well as two spectral identification problems based on the two scores. We propose several index-based algorithms for the two problems. Both theoretical and experimental analyses show that the index-based algorithms significantly improve on speed when compared with existing algorithms.
authors.affiliation: Department of Computer Science and Engineering, University of California, San Diego, California 92093, USA. xil018@cs.ucsd.edu
authors.forename: Xiaowen
authors.initials: X
authors.lastname: Liu
authors.forename: Alessandro
authors.initials: A
authors.lastname: Mammana
authors.forename: Vineet
authors.initials: V
authors.lastname: Bafna
mesh_terms: D000465:Algorithms; D006801:Humans; D010455:Peptides / Q000737:chemistry*; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010455:Peptides; D011506:Proteins