title: Mass spectrometry-based quantification.
abstract: OBJECTIVE
  This review describes the most common methods currently used for mass spectrometry-based quantification in proteomic applications.
  
  
  METHODS
  Quantification can be performed using either labeled or unlabeled approaches. Labeled approaches rely on mass-tagging of peptide reference standards either by direct synthesis or through chemical or metabolic means. Following labeling, samples are pooled and analyzed as one, thereby circumventing any potential error that could result from run-to-run variability. Unlabeled approaches rely on run-to-run comparisons between test and reference samples and assume a highly reproducible separation and similar sample compositions.
  
  
  RESULTS
  A number of commercial labeling reagents are now available and each of these are described along with their strengths and limitations.
  
  
  CONCLUSIONS
  The choice of method will ultimately depend, not just on financial considerations, but also on the context of the experiment.
authors.affiliation: Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3.
authors.forename: Leroi V
authors.initials: LV
authors.lastname: DeSouza
authors.forename: K W Michael
authors.initials: KW
authors.lastname: Siu
mesh_terms: D002853:Chromatography, Liquid / Q000379:methods*; D019411:Clinical Laboratory Techniques; D019295:Computational Biology; D020869:Gene Expression Profiling; D006801:Humans; D007553:Isotope Labeling; D013677:Medical Laboratory Science; D011506:Proteins / Q000302:isolation & purification; D040901:Proteomics; D012015:Reference Standards; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D011506:Proteins