328
Views
4
CrossRef citations to date
0
Altmetric
Review

Pre-Analytical and Analytical Variability in Absolute Quantitative Mrm-Based Plasma Proteomic Studies

, &
Pages 2837-2856 | Published online: 21 Nov 2013

References

  • Hossain M , RobinsonEW, LiuTet al. Enhanced sensitivity for selected reaction monitoring mass spectrometry-based targeted proteomics using a dual stage electrodynamic ion funnel interface. Mol. Cell. Proteomics10(2), do:10.1074/mcp.M000062-MCP201 (2011).
  • Yates JR , RuseCI, NakorchevskyA. Proteomics by mass spectrometry: approaches, advances, and applications. Annu. Rev. Biomed. Eng. 11, 49–79 (2009).
  • Domon B , AebersoldR. Mass spectrometry and protein analysis. Science312(5771), 212–217 (2006).
  • Han X , AslanianA, YatesJR. Mass spectrometry for proteomics. Curr. Opin. Chem. Biol. 12(5), 483–490 (2008).
  • Ibrahim Y , TangK, TolmachevAV, ShvartsburgAA, SmithR. Improving mass spectrometer sensitivity using a high-pressure electrodynamic ion funnel interface. J. Am. Soc. Mass Spectrom. 17(9), 1299–1305 (2006).
  • Du Y , ParksBA, SohnS, KwastKE, KelleherNL. Top-down approaches for measuring expression ratios of intact yeast proteins using Fourier transform mass spectrometry. Anal. Chem. 78(3), 686–694 (2006).
  • Meng F , CargileBJ, PatrieSM, JohnsonJR, McLoughlinSM, KelleherNL. Processing complex mixtures of intact proteins for direct analysis by mass spectrometry. Anal. Chem. 74(13), 2923–2929 (2002).
  • Kelleher NL , LinHY, ValaskovicGA, AaserudDJ, FridrikssonEK, McLaffertyFW. Top down versus bottom up protein characterization by tandem high-resolution mass spectrometry. J. Am. Chem. Soc. 121(4), 806–812 (1999).
  • Link AJ , EngJ, SchieltzDMet al. Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 17(7), 676–682 (1999).
  • Tabb DL , McDonaldWH, Yates Jr 3rd. DTASelect and contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J. Proteome Res. 1(1), 21–26 (2002).
  • Washburn MP , WoltersD, Yates Jr 3rd. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotech. 19(3), 242–247 (2001).
  • Ong S , MannM. Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 1(5), 252–262 (2005).
  • Schulze WX , UsadelB. Quantitation in mass-spectrometry-based proteomics. Annu. Rev. Plant Biol. 61, 491–516 (2010).
  • Bantscheff M , SchirleM, SweetmanG, RickJ, KusterB. Quantitative mass spectrometry in proteomics: a critical review. Anal. Bioanal. Chem. 389(4), 1017–1031 (2007).
  • Elliott M , SmithD, KuzykM, ParkerCE, BorchersCH. Recent trends in quantitative proteomics. J. Mass Spectrom. 44(12), 1637–1660 (2009).
  • Picotti P , AebersoldR. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat. Methods9(6), 555–566 (2012).
  • Gygi SP , RistB, GerberSA, TurecekF, GelbMH, AebersoldR. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechol. 17(10), 994–999 (1999).
  • Ross PL , HuangYN, MarcheseJNet al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics3(12), 1154–1169 (2004).
  • Dayon L , SanchezJC. Relative protein quantification by MS/MS using the tandem mass tag technology. Methods Mol. Biol. 893, 115–127 (2012).
  • Gerber SA , RushJ, StemmanO, KirschnerMW, GygiSP. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl Acad. Sci. USA100(12), 6940–6945 (2003).
  • Huttenhain R , MalmstromJ, PicottiP, AebersoldR. Perspectives of targeted mass spectrometry for protein biomarker verification. Curr. Opin. Chem. Biol. 13(5–6), 518–525 (2009).
  • Brun V , MasselonC, GarinJ, DupuisA. Isotope dilution strategies for absolute quantitative proteomics. J. Proteomics72, 740–749 (2009).
  • Anderson L , HunterCL. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell. Proteomics5(4), 573–588 (2006).
  • Abdi F , QuinnJF, JankovicJet al. Detection of biomarkers with a multiplex quantitative proteomic platform in cerebrospinal fluid of patients with neurodegenerative disorders. J. Alzheimers Dis. 9(3), 293–348 (2006).
  • Elschenbroich S , IgnatchenkoV, ClarkeBet al. In-depth proteomics of ovarian cancer ascites: combining shotgun proteomics and selected reaction monitoring mass spectrometry. J. Proteome Res. 10(5), 2286–2299 (2011).
  • Beaglehole R , BonitaR, HortonRet al. Priority actions for the non-communicable disease crisis. Lancet377(9775), 1438–1447 (2011).
  • Mathers CD , LoncarD. Projections of global mortality and burden of disease from 2002 to 2030. PLoS Med. 3(11), e442 (2006).
  • Verma S , YehET. C-reactive protein and atherothrombosis – beyond a biomarker: an actual partaker of lesion formation. Am. J. Physiol. Regul. Integr. Comp. Physiol. 5(285), 5 (2003).
  • Zakynthinos E , PappaN. Inflammatory biomarkers in coronary artery disease. J. Cardiol. 53, 53(3), 317–333 (2009).
  • Anderson NL , AndersonNG. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics1(11), 845–867 (2002).
  • Brun V , DupuisA, AdraitAet al. Isotope-labeled protein standards: toward absolute quantitative proteomics. Mol. Cell. Proteomics6(12), 2139–2149 (2007).
  • Lebert D , DupuisA, GarinJ, BruleyC, BrunV. Production and use of stable isotope-labeled proteins for absolute quantitative proteomics. Methods Mol. Biol. 753, 93–115 (2011).
  • Kirkpatrick DS , GerberSA, GygiSP. The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods35(3), 265–273 (2005).
  • Kettenbach AN , RushJ, GerberSA. Absolute quantification of protein and post-translational modification abundance with stable isotope-labeled synthetic peptides. Nat. Protoc. 6(2), 175–186 (2011).
  • Percy AJ , ChambersAG, YangJ, BorchersCH. Multiplexed MRM-based quantitation of candidate cancer biomarker proteins in undepleted and non-enriched human plasma. Proteomics13(14), 2202–2215 (2013).
  • Percy AJ , ChambersAG, YangJ, DomanskiD, BorchersCH. Comparison of standard-flow and nano-flow liquid chromatography systems for MRM-based quantitation of putative plasma biomarker proteins. Anal. Bioanal. Chem. 404(4), 1089–1101 (2012).
  • Chambers AG , PercyAJ, YangJ, CamenzindAG, BorchersCH. Multiplexed quantitation of endogenous proteins in dried blood spots by multiple reaction monitoring mass spectrometry. Mol. Cell. Proteomics12(3), 781–791 (2013).
  • Domanski D , PercyAJ, YangJet al. MRM-based multiplexed quantitation of 67 putative cardiovascular disease biomarkers in human plasma. Proteomics12(8), 1222–1243 (2012).
  • Kuzyk MA , SmithD, YangJet al. Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma. Mol. Cell. Proteomics8(8), 1860–1877 (2009).
  • Keshishian H , AddonaT, BurgessM, KuhnE, CarrSA. Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell. Proteomics6, 2212–2229 (2007).
  • Keshishian H , AddonaT, BurgessMet al. Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell. Proteomics8, 2339–2349 (2009).
  • Rezeli M , VégváriA, OttervaldJ, OlssonT, LaurellT, Marko-VargaG. MRM assay for quantitation of complement components in human blood plasma – a feasibility study on multiple sclerosis. J. Proteomics75(1), 211–220 (2011).
  • Liu T , HossainM, SchepmoesAAet al. Analysis of serum total and free PSA using immunoaffinity depletion coupled to MRM: correlation with clinical immunoassay tests. J. Proteomics75(15), 4747–4757 (2012).
  • Hüttenhain R , SosteM, SelevsekNet al. Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics. Sci. Transl. Med. 4(142), 1–13 (2012).
  • Razavi M , FrickLE, LaMarrWAet al. High-throughput SISCAPA quantitation of peptides from human plasma digests by ultrafast, liquid chromatography-free mass spectrometry. J. Proteome Res. 11(12), 5642–5649 (2012).
  • Whiteaker JR , ZhaoL, AndersonL, PaulovichAG. An automated and multiplexed method for high throughput peptide immunoaffinity enrichment and multiple reaction monitoring mass spectrometry-based quantification of protein biomarkers. Mol. Cell. Proteomics9(1), 184–196 (2010).
  • Kuhn E , AddonaT, KeshishianHet al. Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry. Clin. Chem. 55(6), 1108–1117 (2009).
  • Shi T , FillmoreTL, SunXet al. Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum. Proc. Natl Acad. Sci. USA109(38), 15395–15400 (2012).
  • Lundblad RL . Considerations for the use of blood plasma and serum for proteomic analysis. The Internet Journal of Genomics and Proteomics. 1(2) doi:10.5580 (2005).
  • Lippi G , FranchiniM, MontagnanaM, SalvagnoGL, PoliG, GuidiGC. Quality and reliability of routine coagulation testing: can we trust that sample? Blood Coagul. Fibrinolysis17(7), 513–519 (2006).
  • Gelfand CA , OmennGS. Pre-analytical variables for plasma and serum proteome analyses. In:Sample Preparation in Biological Mass Spectrometry. Ivanov AR, Lazarev AV (Eds). Springer, Heidelberg, Germany, 269–290 (2011).
  • Lista S , FaltracoF, HampelH. Biological and methodical challenges of blood-based proteomics in the field of neurological research. Prog. Neurobiol. 101–102, 18–34 (2013).
  • Rai AJ , VitzthumF. Effects of pre-analytical variables on peptide and protein measurements in human serum and plasma: implications for clinical proteomics. Expert Rev. Proteomics3(4), 409–426 (2006).
  • Yi J , CraftD, GelfandCA. Minimizing pre-analytical variation of plasma samples by proper blood collection and handling. Methods Mol. Biol. 728, 137–149 (2011).
  • Rodriguez H , TežakZ, MesriMet al. Analytical validation of protein-based multiplex assays: a workshop report by the NCI-FDA Interagency Oncology Task Force on Molecular Diagnostics. Clin. Chem. 56(2), 237–243 (2010).
  • Paulovich AG , BillheimerDD, Ham A-JLet al. A CPTAC inter-laboratory study characterizing a yeast performance standard for benchmarking LC–MS platform performance. Mol. Cell. Proteomics9, 242–254 (2010).
  • Rodriguez H , RiversR, KinsingerCet al. Reconstructing the pipeline by introducing multiplexed multiple reaction monitoring mass spectrometry for cancer biomarker verification: an NCI-CPTC initiative perspective. Proteomics Clin. Appl. 4(12), 904–914 (2010).
  • Kinsinger CR , ApffelJ, BakerMet al. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). J. Proteome Res. 11(2), 1412–1419 (2011).
  • Addona TA , AbbatielloSE, SchillingBet al. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat. Biotechnol. 27(7), 633–641 (2009).
  • Proc JL , KuzykMA, HardieDBet al. A quantitative study of the effects of chaotropic agents, surfactants, and solvents on the digestion efficiency of human plasma proteins by trypsin. J. Proteome Res. 9(10), 5422–5437 (2010).
  • Benoy I , SalgadoR, ColpaertC, WeytjensR, VermeulenPB, DirixLY. Serum interleukin 6, plasma VEGF, serum VEGF, and VEGF platelet load in breast cancer patients. Clin. Breast Cancer2(4), 311–315 (2002).
  • Caisey JD , KingDJ. Clinical chemical values for some common laboratory animals. Clin. Chem. 26(13), 1877–1879 (1980).
  • Omenn GS , StatesDJ, AdamskiMet al. Overview of the HUPO plasma proteome project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics5(13), 3226–3245 (2005).
  • Omenn GS . The HUPO human plasma proteome project. Proteomics Clin. Appl. 1(8), 769–779 (2007).
  • Omenn GS . The Human Proteome Organization Plasma Proteome Project pilot phase: reference specimens, technology platform comparisons, and standardized data submissions and analyses. Proteomics4, 1235–1240 (2004).
  • Ohlund LB , HardieDB, ElliottMHet al. Standard operating procedures and protocols for the preparation and analysis of plasma samples using the iTRAQ methodology. In:Sample Preparation in Biological Mass Spectrometry. Ivanov A, Lazarev A (Eds). Springer, NY, USA, 575–624 (2011).
  • O’Mullan P , CraftD, YiJ, GelfandCA. Thrombin induces broad spectrum proteolysis in human serum samples. Clin. Chem. Lab. Med. 47(6), 685–693 (2009).
  • Rai AJ , GelfandCA, HaywoodBCet al. HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples. Proteomics5, 3262–3277 (2005).
  • Hulmes JD , BetheaD, HoKet al. An investigation of plasma collection, stabilization, and storage procedures for proteomic analysis of clinical samples. Clin. Proteomics1(1), 17–31 (2004).
  • Yi J , KimC, GelfandCA. Inhibition of intrinsic proteolytic activities moderates pre-analytical variability and instability of human plasma. J. Proteome Res. 6(5), 1768–1781 (2007).
  • Aguilar-Mahecha A , KuzykMA, DomanskiD, BorchersCH, BasikM. Comparison of blood collection tubes and processing protocols for plasma proteomics studies. PLoS ONE7(6), e38290 (2012).
  • Zimmerman LJ , LiM, YarbroughWG, SlebosRJ, LieblerDC. Global stability of plasma proteomes for mass spectrometry-based analyses. Mol. Cell. Proteomics11(6), M111.014340 (2012).
  • Randall SA , McKayMJ, PascoviciDet al. Remarkable temporal stability of high-abundance human plasma proteins assessed by targeted mass spectrometry. Proteomics Clin. Appl. 6(11–12), 626–634 (2012).
  • Ostroff R , ForemanT, KeeneyTR, StratfordS, WalkerJJ, ZichiD. The stability of the circulating human proteome to variations in sample collection and handling procedures measured with an aptamer-based proteomics array. J. Proteomics73, 649–666 (2010).
  • Aziz N , NishanianP, MitsuyasuR, DetelsR, FaheyJL. Variables that affect assays for plasma cytokines and soluble activation markers. Clin. Diagn. Lab. Immunol. 6(1), 89–95 (1999).
  • Martino TA , TataN, BjarnasonGA, StraumeM, SoleMJ. Diurnal protein expression in blood revealed by high throughput mass spectrometry proteomics and implications for translational medicine and body. Am. J. Physiol. Regul. Integr. Comp. Physiol. 293, R1430–R1437 (2007).
  • Robles MS , MannM. Proteomic approaches in circadian biology. Handb. Exp. Pharmacol. 217, 389–407 (2013).
  • Ito Y , NakachiK, ImaiKet al. Stability of frozen serum levels of insulin-like growth factor-I, insulin-like growth factor-II, insulin-like growth factor binding protein-3, transforming growth factor beta, soluble Fas, and superoxide dismutase activity for the JACC study. J. Epidemiol. 15(Suppl. 1), S67–S73 (2005).
  • Insenser M , Martínez-GarcíaM, NietoRM, San-MillánJL, Escobar-MorrealeHF. Impact of the storage temperature on human plasma proteomic analysis: implications for the use of human plasma collections in research. Proteomics Clin. Appl. 4(8–9), 739–744 (2010).
  • Markiewski MM , NilssonB, EkdahlKN, MollnesTE, LambrisJD. Complement and coagulation: strangers or partners in crime? Trends Immunol. 28, 184–192 (2007).
  • Murphy BM , SwartsS, MuellerBM, van der Geer P, Manning MC, Fitchmun MI. Protein instability following transport or storage on dry ice. Nat. Methods10(4), 278–279 (2013).
  • Betsou F , Beaudeux J-L, Berthelaix Aet al. Procédure pour tester l’impact des variables préanalytiques sur des analyses peptidiques et protéiques et proposition de codage des procédures préanalytiques. Ann. Biol. Clin. (Paris)67(6), 641–649 (2009).
  • Tuck MK , ChanDW, ChiaDet al. Standard operating procedures for serum and plasma collection: early detection research network consensus statement standard operating procedure integration working group. J. Proteome Res. 8, 113–117 (2009).
  • Polaskova V , KapurA, KhanA, MolloyMP, BakerMS. High-abundance protein depletion: comparison of methods for human plasma biomarker discovery. Electrophoresis31(3), 471–482 (2010).
  • Anderson NL , AndersonNG, HainesLR, HardieDB, OlafsonRW, PearsonTW. Mass spectrometric quantitation of peptides and proteins using stable isotope standards and capture by anti-peptide antibodies (SISCAPA). J. Proteome Res. 3(2), 235–244 (2004).
  • Anderson NL , JacksonA, SmithD, HardieD, BorchersC, PearsonTW. SISCAPA peptide enrichment on magnetic beads using an in-line bead trap device. Mol. Cell. Proteomics8(5), 995–1005 (2009).
  • Whiteaker JR , ZhaoL, AbbatielloSEet al. Evaluation of large scale quantitative proteomic assay development using peptide affinity-based mass spectrometry. Mol. Cell. Proteomics10(4), M110.005645 (2011).
  • Schoenherr RM , ZhaoL, WhiteakerJRet al. Automated screening of monoclonal antibodies for SISCAPA assays using a magnetic bead processor and liquid chromatography-selected reaction monitoring-mass spectrometry. J Immunol. Methods353(1–2), 49–61 (2010).
  • Jiang J , ParkerCE, FullerJR, KawulaTH, BorchersCH. An immunoaffinity tandem mass spectrometry (iMALDI) assay for detection of Francisella tularensis. Anal. Chim. Acta605, 70–79. (2007).
  • Jiang J , ParkerCE, HoadleyKA, PerouCM, BoysenG, BorchersCH. Development of an immuno tandem mass spectrometry (iMALDI) assay for EGFR diagnosis. Proteomics Clin. Appl. 1, 1651–1659 (2007).
  • Reid JD , HolmesDT, MasonDR, ShahB, BorchersCH. Towards the development of an immuno MALDI (iMALDI) mass spectrometry assay for the diagnosis of hypertension. J. Am. Soc. Mass Spectrom. 21(10), 1680–1686 (2010).
  • Mason DR , ReidJD, CamenzindAG, HolmesDT, BorchersCH. Duplexed iMALDI for the detection of angiotensin I and angiotensin II. Methods56(2), 213–222 (2012).
  • Polaskova V , KapurA, KhanA, MolloyMP, BakerMS. High-abundance protein depletion: comparison of methods for human plasma biomarker discovery. Electrophoresis31(3), 471–482 (2010).
  • Kim K , YuJ, MinHet al. Online monitoring of immunoaffinity-based depletion of high-abundance blood proteins by UV spectrophotometry using enhanced green fluorescence protein and FITC-labeled human serum albumin. Proteome Sci. 8, 62 (2010).
  • Olsen JV , OngSE, MannM. Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol. Cell. Proteomics3(6), 608–614 (2004).
  • Picotti P , AebersoldR, DomonB. The implications of proteolytic background for shotgun proteomics. Mol. Cell. Proteomics6(9), 1589–1598 (2007).
  • Lin S , YaoG, QiDet al. Fast and efficient proteolysis by microwave-assisted protein digestion using trypsin-immobilized magnetic silica microspheres. Anal. Chem. 80(10), 3655–3665 (2008).
  • Wang N , LiL. Reproducible microwave-assisted acid hydrolysis of proteins using a household microwave oven and its combination with LC–ESI-MS/MS for mapping protein sequences and modifications. J. Am. Soc. Mass Spectrom. 21(9), 1573–1587 (2010).
  • Ye X , LiL. Microwave-assisted protein solubilization for mass spectrometry-based shotgun proteome analysis. Anal. Chem. 84(14), 6181–6191 (2012).
  • López-Ferrer D , CapeloJL, VázquezJ. Ultra fast trypsin digestion of proteins by high intensity focused ultrasound. J. Proteome Res. 4, 1569–1574 (2005).
  • López-Ferrer D , PetritisK, HixsonKKet al. Application of pressurized solvents for ultrafast trypsin hydrolysis in proteomics: proteomics on the fly. J. Proteome Res. 7(8), 3276–3281 (2008).
  • López-Ferrer D , PetritisK, LouretteNMet al. On-line digestion system for protein characterization and proteome analysis. Anal. Chem. 23, 8930–8936 (2008).
  • Glatter T , LudwigC, AhrnéE, AebersoldR, HeckAJ, SchmidtA. Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem LysC/trypsin proteolysis over trypsin digestion. J. Proteome Res. 11(11), 5145–5156 (2012).
  • Canas B , PineiroC, CalvoE, Lopez-FerrerD, GallardoJM. Trends in sample preparation for classical and second generation proteomics. J. Chromatog. A1153, 235–258 (2007).
  • Zhou J , ZhouTY, CaoRet al. Evaluation of the application of sodium deoxycholate to proteomic analysis of rat hippocampal plasma membrane.rat hippocampal plasma membrane. J. Proteome Res. 5, 2547–2553 (2006).
  • Lin Y , ZhouJ, BiD, ChenP, WangX, LiangS. Sodium-deoxycholate-assisted tryptic digestion and identification of proteolytically resistant proteins. Anal. Biochem. 377(2), 259–266 (2008).
  • Burkhart JM , SchumbrutzkiC, WortelkampS, SickmannA, ZahediRP. Systematic and quantitative comparison of digest efficiency and specificity reveals the impact of trypsin quality on MS-based proteomics. J. Proteomics75(4), 1454–1462 (2012).
  • Keil B . Specificity of Proteolysis. Springer-Verlag, Berlin, Germany (1992).
  • Rodriguez J , GuptaN, SmithRD, PevznerPA. Does trypsin cut before proline? J. Proteome Res. 7(1), 300–305 (2008).
  • Domanski D , Cohen Freue G, Sojo Let al. The use of multiplexed MRM for the discovery of biomarkers to differentiate iron-deficiency anemia from anemia of inflammation. J. Proteomics75(12), 3514–3528 (2012).
  • Domanski D , SmithDS, MillerCAet al. High-flow multiplexed MRM-based analysis of proteins in human plasma without depletion or enrichment. Clin. Lab. Med. 31(3), 371–384 (2011).
  • Gillette MA , CarrSA. Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry. Nat. Methods10, 28–34 (2013).
  • Kuhn E , WhiteakerJR, ManiDRet al. Interlaboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma. Mol. Cell. Proteomics11(6), M111.013854 (2012).
  • Dupuis A , HennekinneJA, GarinJ, BrunV. Protein standard absolute quantification (PSAQ) for improved investigation of staphylococcal food poisoning outbreaks. Proteomics8(22), 4633–4636 (2008).
  • Jaquinod M , TrauchessecM, HuilletCet al. Mass spectrometry-based absolute protein quantification: PSAQ™ strategy makes use of “noncanonical” proteotypic peptides. Proteomics12(8), 1217–1221 (2012).
  • Huillet C , AdraitA, LebertDet al. Accurate quantification of cardiovascular biomarkers in serum using Protein Standard Absolute Quantification (PSAQ™) and selected reaction monitoring. Mol. Cell. Proteomics11(2), M111.008235 (2012).
  • Agger SA , MarneyLC, HoofnagleAN. Simultaneous quantification of apolipoprotein a-I and apolipoprotein B by liquid chromatography–multiple reaction monitoring–mass spectrometry. Clin. Chem. 56(12), 1804–1813 (2010).
  • Hoofnagle AN , WenerMH. The fundamental flaws of immunoassays and potential solutions using tandem mass spectrometry. J. Immunol. Methods347(1–2), 3–11 (2009).
  • Browne TR . Stable isotopes in pharmacology studies: present and future. J. Clin. Pharmacol. 26(6), 485–489 (1986).
  • Parsons HG . Stable isotopes in the management and diagnosis of inborn errors of metabolism. Can. J. Physiol. Pharmacol. 68(7), 950–954 (1990).
  • Picard G , LebertD, LouwagieMet al. PSAQ™ standards for accurate MS-based quantification of proteins: from the concept to biomedical applications. J. Mass Spectrom. 47(10), 1353–1363 (2012).
  • Picotti P , BodenmillerB, MuellerLN, DomonB, AebersoldR. Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell138(4), 795–806 (2009).
  • Fortin T , SalvadorA, CharrierJPet al. Multiple reaction monitoring cubed for protein quantification at the low nanogram/milliliter level in nondepleted human serum. Anal. Chem. 81(22), 9343–9352 (2009).
  • Hunter C . MRM3 quantitation for highest selectivity of proteins in complex matrices. J. Biomol. Tech. 21(3 Suppl.), S34–S35 (2010).
  • Shi T , SuD, LiuTet al. Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics. Proteomics12(8), 1074–1092 (2012).
  • Percy AJ , ChambersAG, ParkerCE, BorchersCH. Absolute quantitation of proteins in human blood by multiplexed multiple reaction monitoring mass spectrometry. Methods Mol. Biol. 1000, 167–189 (2013).
  • Abbatiello SE , ManiDR, KeshishianH, CarrSA. Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry. Clin. Chem. 56(2), 291–305 (2010).
  • Kiyonami R , SchoenA, PrakashAet al. Increased selectivity, analytical precision, and throughput in targeted proteomics. Mol. Cell. Proteomics10(2), M110.002931 (2011).
  • Röst H , MalmströmL, AebersoldR. A computational tool to detect and avoid redundancy in selected reaction monitoring. Mol. Cell. Proteomics11(8), 540–549 (2012).
  • Gillet LC , NavarroP, TateSet al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol. Cell. Proteomics11(6), O111.016717 (2012).
  • Hoofnagle AN . Quantitative clinical proteomics by liquid chromatography–tandem mass spectrometry: assessing the platform. Clin. Chem. Lab. Med. 56(2), 161–164 (2010).
  • Lehmann S , HoofnagleA, HochstrasserDet al. Quantitative clinical chemistry proteomics (qCCP) using mass spectrometry: general characteristics and application. Clin. Chem. Lab. Med. 51(5), 919–935 (2013).
  • Gallien S , DuriezE, DemeureK, DomonB. Selectivity of LC–MS/MS analysis: implication for proteomics experiments. J. Proteomics81, 148–158 (2013).
  • Boja ES , JortaniSA, RitchieJet al. The journey to regulation of protein-based multiplex quantitative assays. Clin. Chem. 57(4), 560–567 (2011).
  • Bell AW , DeutschEW, AuCEet al. A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nat. Methods6(6), 423–430 (2009).
  • Hermjakob H . The HUPO proteomics standards initiative – overcoming the fragmentation of proteomics data. Proteomics6(Suppl. 2), 34–38 (2006).
  • Legrain P , AebersoldR, ArchakovAet al. The human proteome project: current state and future direction. Mol. Cell. Proteomics10(7), M111.00993 (2011).
  • Wright GW , CazaresLH, LeungSMet al. Proteinchip(R) surface enhanced laser desorption/ionization (SELDI) mass spectrometry: a novel protein biochip technology for detection of prostate cancer biomarkers in complex protein mixtures. Prostate Cancer Prostatic Dis. 2(5/6), 264–276 (1999).
  • Petricoin EF , ArdekaniAM, HittBAet al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet359(9306), 572–577 (2002).
  • Baggerly KA , MorrisJS, CoombesKR. Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. Bioinformatics20(5), 777–785 (2003).
  • Prakash A , RezaiT, KrastinsBet al. Platform for establishing interlaboratory reproducibility of selected reaction monitoring-based mass spectrometry peptide assays. J. Proteome Res. 9(12), 6678–6688 (2010).
  • Percy AJ , ChambersAG, SmithDS, BorchersCH. Standardized protocols for quality control of MRM-based plasma proteomic workflow. J. Proteome Res. 12(1), 222–233 (2013).

Websites

  • Schoenfeld DA. Statistical Considerations for Clinical Trials and Scientific Experiments. http://hedwig.mgh.harvard.edu/sample_size/size.html#ssize
  • Anderson L, Pope M, Razavi M et al . High sensitivity SISCAPA-based peptide quantitation using UHPLC and the 6490 QQQ with iFunnel technology. www.chem.agilent.com/Library/applications/5990–8999en_lo.pdf
  • Promise. PSAQ™: the ultimate in quantification. www.promise-proteomics.com/technology_promise_proteomics.php
  • Fong T. New Technology Combining Bruker’s MALDI-TOF/TOF with Bio-Rad’s SELDI Set to Launch. www.genomeweb.com/proteomics/new-technology-combining-brukers-maldi-toftof-bio-rads-seldi-set-launch

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.