The future directions for the targeted quantitative proteomics experiment should address a small number of current problems and incorporate new developments in mass spectrometry instrumentation. Two notable problems at this time are the broader acceptance of selected reaction monitoring as a primary method of protein quantitation and at least some improvement in the sensitivity of the analysis. Improvements will always include the continuing evolution of the instruments to have higher resolution, faster scan rates, and better sensitivity. Others improvements will be seen in continued development of the peptide mass spectrometry databases. Progress in each of these areas is inevitable. The most difficult area to predict is the potential for new chemical tools. For example, reagents that improve sample processing or increase the sensitivity of selected classes of peptides can also have a major impact.
KeywordsSelect Reaction Monitoring Quantitative Proteomics Protein Quantitation Immunochemical Method Mass Spectroscopist
- 4.Whiteaker JR, Lin C, Kennedy J, Hou L, Trute M, Sokal I, Yan P, Schoenherr RM, Zhao L, Voytovich UJ, Kelly-Spratt KS, Krasnoselsky A, Gafken PR, Hogan JM, Jones LA, Wang P, Amon L, Chodosh LA, Nelson PS, McIntosh MW, Kemp CJ, Paulovich AG (2011) A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nat Biotechnol 29:625–634PubMedCrossRefGoogle Scholar
- 6.Rodriguez H, Tezak Z, Mesri M, Carr SA, Liebler DC, Fisher SJ, Tempst P, Hiltke T, Kessler LG, Kinsinger CR, Philip R, Ransohoff DF, Skates SJ, Regnier FE, Anderson NL, Mansfield E, Workshop Participants (2010) Analytical validation of protein-based multiplex assays: a workshop report by the NCI-FDA interagency oncology task force on molecular diagnostics. Clin Chem 56:237–243PubMedCrossRefGoogle Scholar
- 7.Regnier FE, Skates SJ, Mesri M, Rodriguez H, Tezak Z, Kondratovich MV, Alterman MA, Levin JD, Roscoe D, Reilly E, Callaghan J, Kelm K, Brown D, Philip R, Carr SA, Liebler DC, Fisher SJ, Tempst P, Hiltke T, Kessler LG, Kinsinger CR, Ransohoff DF, Mansfield E, Anderson NL (2010) Protein-based multiplex assays: mock presubmissions to the US Food and Drug Administration. Clin Chem 56:165–171PubMedCrossRefGoogle Scholar
- 9.Hüttenhain R, Surinova S, Ossola R, Sun Z, Campbell D, Cerciello F, Schiess R, Bausch-Fluck D, Rosenberger G, Chen J, Rinner O, Kusebauch U, Hajdúch M, Moritz RL, Wollscheid B, Aebersold R (2013) N-glycoprotein SRMAtlas: a resource of mass spectrometric assays for N-glycosites enabling consistent and multiplexed protein quantification for clinical applications. Mol Cell Proteomics 12:1005–1016PubMedCrossRefGoogle Scholar