Surrogate peptide selection and internal standardization for accurate quantification of endogenous proteins

Papers of special note have been highlighted as: • of interest; •• of considerable interest

References

• 1. Calderón‐Celis F, Encinar JR, Sanz‐Medel A. Standardization approaches in absolute quantitative proteomics with mass spectrometry. Mass. Spectrom. Rev. 37(6), 715–737 (2018). •• Provides critical analytical insight into different standardization approaches for absolute quantitative proteomics (molecular and elemental).
  Medline CASGoogle Scholar
• 2. Bush L. The challenge of accurate protein bioanalysis. 12(22), 16–18 (2016).
  Google Scholar
• 3. Coorssen JR, Yergey AL. Proteomics is analytical chemistry: fitness-for-purpose in the application of top-down and bottom-up analyses. Proteomes 3(4), 440–453 (2015).
  Medline CASGoogle Scholar
• 4. Van De Merbel NC. Protein quantification by LC–MS: a decade of progress through the pages of Bioanalysis. Bioanalysis 11(07), 629–644 (2019).
  Google Scholar
• 5. Gillet LC, Leitner A, Aebersold R. Mass spectrometry applied to bottom-up proteomics: entering the high-throughput era for hypothesis testing. Annu. Rev. Anal. Chem. 9, 449–472 (2016).
  MedlineGoogle Scholar
• 6. Dupree EJ, Jayathirtha M, Yorkey H, Mihasan M, Petre BA, Darie CC. A critical review of bottom-up proteomics: the good, the bad, and the future of this field. Proteomes 8(3), 14 (2020).
  Medline CASGoogle Scholar
• 7. Ankney JA, Muneer A, Chen X. Relative and absolute quantitation in mass spectrometry-based proteomics. Annu. Rev. Anal. Chem. 11, 49–77 (2018).
  Medline CASGoogle Scholar
• 8. Elliott MH, Smith DS, Parker CE, Borchers C. Current trends in quantitative proteomics. J. Mass. Spectrom. 44(12), 1637–1660 (2009).
  Medline CASGoogle Scholar
• 9. Mermelekas G, Vlahou A, Zoidakis J. SRM/MRM targeted proteomics as a tool for biomarker validation and absolute quantification in human urine. Expert Rev. Mol. Diagn. 15(11), 1441–1454 (2015).
  MedlineGoogle Scholar
• 10. Li F, Fast D, Michael S. Absolute quantitation of protein therapeutics in biological matrices by enzymatic digestion and LC–MS. Bioanalysis 3(21), 2459–2480 (2011).
  CASGoogle Scholar
• 11. Pagel O, Loroch S, Sickmann A, Zahedi RP. Current strategies and findings in clinically relevant post-translational modification-specific proteomics. Expert Rev. Proteomics 12(3), 235–253 (2015).
  Medline CASGoogle Scholar
• 12. Chao T-C, Hansmeier N, Halden RU. Towards proteome standards: the use of absolute quantitation in high-throughput biomarker discovery. J. Proteomics 73(8), 1641–1646 (2010).
  Medline CASGoogle Scholar
• 13. Cho WC. Proteomics technologies and challenges. Genomics Proteomics Bioinformatics 5(2), 77–85 (2007).
  Medline CASGoogle Scholar
• 14. Rivers J, Simpson DM, Robertson DH, Gaskell SJ, Beynon RJ. Absolute multiplexed quantitative analysis of protein expression during muscle development using QconCAT. Mol. Cell. Proteomics. 6(8), 1416–1427 (2007).
  Medline CASGoogle Scholar
• 15. Chiva C, Sabido E. Peptide selection for targeted protein quantitation. J. Proteome Res. 16(3), 1376–1380 (2017).
  Medline CASGoogle Scholar
• 16. Prasad B, Unadkat JD. Optimized approaches for quantification of drug transporters in tissues and cells by MRM proteomics. AAPS J. 16(4), 634–648 (2014).
  Medline CASGoogle Scholar
• 17. Kamiie J, Ohtsuki S, Iwase R et al. Quantitative atlas of membrane transporter proteins: development and application of a highly sensitive simultaneous LC/MS/MS method combined with novel in-silico peptide selection criteria. Pharm. Res. 25(6), 1469–1483 (2008).
  Medline CASGoogle Scholar
• 18. Gröer C, Brück S, Lai Y et al. LC–MS/MS-based quantification of clinically relevant intestinal uptake and efflux transporter proteins. J. Pharm. Biomed. Anal. 85, 253–261 (2013)
  Medline CASGoogle Scholar
• 19. Chen Y, Wang F, Xu F, Yang T. Mass spectrometry-based protein quantification. 255–279 (2016).
  Google Scholar
• 20. Maclean B, Tomazela DM, Shulman N et al. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26(7), 966–968 (2010).
  Medline CASGoogle Scholar
• 21. Deutsch EW, Lam H, Aebersold R. PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 9(5), 429–434 (2008).
  Medline CASGoogle Scholar
• 22. Fenyö D, Beavis RC. The GPMDB rest interface. Bioinformatics 31(12), 2056–2058 (2015).
  MedlineGoogle Scholar
• 23. Kusebauch U, Deutsch EW, Campbell DS, Sun Z, Farrah T, Moritz RL. Using PeptideAtlas, SRMAtlas, and PASSEL: comprehensive resources for discovery and targeted proteomics. Curr. Protoc. Bioinformatics. 46(1), 13.25.11–13.25.28 (2014).
  Google Scholar
• 24. Mead JA, Bianco L, Ottone V et al. MRMaid, the web-based tool for designing multiple reaction monitoring (MRM) transitions. Mol. Cell. Proteomics 8(4), 696–705 (2009).
  Medline CASGoogle Scholar
• 25. Kirkpatrick DS, Gerber SA, Gygi SP. The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods 35(3), 265–273 (2005).
  Medline CASGoogle Scholar
• 26. Yuan L, Zhu MJM. Quantitative bioanalysis of proteins by mass spectrometry. Methods Mol. Biol. 5, 1–10 (2015).
  Google Scholar
• 27. Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL. NCBI BLAST: a better web interface. Nucleic Acids Res. 36(Suppl. 2), W5–W9 (2008).
  Medline CASGoogle Scholar
• 28. Hustoft HK, Malerod H, Wilson SR, Reubsaet L, Lundanes E, Greibrokk T. A critical review of trypsin digestion for LC-MS based proteomics. Methods Mol. Biol. 73 (2012).
  Google Scholar
• 29. Luque-Garcia JL, Neubert TA. On-membrane tryptic digestion of proteins for mass spectrometry analysis. Methods Mol. Biol. Springer, 331–341 (2009). • Demonstrates the suitability of use of recombinant stable isotope labeled proteins as internal standards over stable isotope labeled peptides.
  Google Scholar
• 30. Shuford CM, Walters JJ, Holland PM et al. Absolute protein quantification by mass spectrometry: not as simple as advertised. Anal. Chem. 89(14), 7406–7415 (2017).
  Medline CASGoogle Scholar
• 31. Brownridge P, Beynon RJ. The importance of the digest: proteolysis and absolute quantification in proteomics. Methods 54(4), 351–360 (2011).
  Medline CASGoogle Scholar
• 32. Bhatt DK, Prasad B. Critical issues and optimized practices in quantification of protein abundance level to determine interindividual variability in DMET proteins by LC‐MS/MS proteomics. Clin. Pharmacol. Ther. 103(4), 619–630 (2018).
  Medline CASGoogle Scholar
• 33. Arnold SL, Stevison F, Isoherranen N. Impact of sample matrix on accuracy of peptide quantification: assessment of calibrator and internal standard selection and method validation. Anal. Chem. 88(1), 746–753 (2016).
  Medline CASGoogle Scholar
• 34. Wang X, Liang Y, Liu L, Shi J, Zhu HJ. Targeted absolute quantitative proteomics with SILAC internal standards and unlabeled full‐length protein calibrators (TAQSI). Rapid Commun. Mass Spectrom. 30(5), 553–561 (2016).
  Medline CASGoogle Scholar
• 35. Vandermarliere E, Mueller M, Martens L. Getting intimate with trypsin, the leading protease in proteomics. Mass Spectrom. Rev. 32(6), 453–465 (2013).
  Medline CASGoogle Scholar
• 36. Chen Q, Jiang Y, Ren Y, Ying M, Lu B. Peptide selection for accurate targeted protein quantification via a dimethylation high-resolution mass spectrum strategy with a peptide release kinetic model. ACS Omega. 5(8), 3809–3819 (2020). • Describes a workflow of peptide selection to determine proteotypic peptides using a dimethylation high-resolution mass spectrum strategy with a peptide release kinetic model.
  Medline CASGoogle Scholar
• 37. Lawless C, Hubbard SJ. Prediction of missed proteolytic cleavages for the selection of surrogate peptides for quantitative proteomics. OMICS 16(9), 449–456 (2012).
  Medline CASGoogle Scholar
• 38. Pratt JM, Simpson DM, Doherty MK, Rivers J, Gaskell SJ, Beynon RJ. Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Nat. Protoc. 1(2), 1029–1043 (2006).
  Medline CASGoogle Scholar
• 39. Modiwala M, Jadav T, Sahu AK, Tekade RK, Sengupta P. A critical review on advancement in analytical strategies for the quantification of clinically relevant biological transporters. Crit. Rev. Anal. Chem. doi: 10408347.2021.1891859 (2021) (Epub ahead of print).
  MedlineGoogle Scholar
• 40. Maaß S, Becher D. Absolute protein quantification using AQUA-calibrated 2D-PAGE. Microbial Proteomics. 141–162 (2018).
  Google Scholar
• 41. Zimmer D, Schneider K, Sommer F, Schroda M, Mühlhaus T. Artificial intelligence understands peptide observability and assists with absolute protein quantification. Front. Plant Sci. 9, 1559 (2018). •• Described a wide variety of methods, reagents, instrumentations and data analysis tools available to design peptidomic experiments.
  MedlineGoogle Scholar
• 42. Pailleux F, Beaudry F. Internal standard strategies for relative and absolute quantitation of peptides in biological matrices by liquid chromatography tandem mass spectrometry. Biomed. Chromatogr. 26(8), 881–891 (2012).
  Medline CASGoogle Scholar
• 43. Domon B, Aebersold R. Options and considerations when selecting a quantitative proteomics strategy. Nat. Biotechnol. 28(7), 710–721 (2010).
  Medline CASGoogle Scholar
• 44. Brun V, Masselon C, Garin J, Dupuis A. Isotope dilution strategies for absolute quantitative proteomics. J. Proteomics. 72(5), 740–749 (2009).
  Medline CASGoogle Scholar
• 45. Lebert D, Dupuis A, Garin J, Bruley C, Brun V. Production and use of stable isotope-labeled proteins for absolute quantitative proteomics. Methods Mol Biol. 93–115 (2011).
  MedlineGoogle Scholar
• 46. Ong S-E, Blagoev B, Kratchmarova I, Foster LJ, Andersen JS, Mann M. Stable isotope labeling by amino acids in cell culture for quantitative proteomics. Adv Exp Med Biol. Elsevier, 427–436 (2006).
  Google Scholar
• 47. Oeckl P, Steinacker P, Otto M. Comparison of internal standard approaches for SRM analysis of alpha-synuclein in cerebrospinal fluid. J. Proteome Res. 17(1), 516–523 (2018).
  Medline CASGoogle Scholar
• 48. Faria M, Halquist M. Internal standards for absolute quantification of large molecules (proteins) from biological matrices by LC-MS/MS. 61 (2018). •• Reports a systematic investigation of two important aspects of peptide and protein quantification by LC–MS/MS, the enzymatic digestion step and the internal standardization approach.
  Google Scholar
• 49. Bronsema KJ, Bischoff R, Van De Merbel N. High-sensitivity LC-MS/MS quantification of peptides and proteins in complex biological samples: the impact of enzymatic digestion and internal standard selection on method performance. Anal. Chem. 85(20), 9528–9535 (2013).
  Medline CASGoogle Scholar
• 50. Winther B, Moi P, Nordlund MS, Lunder N, Paus E, Reubsaet JL. Absolute ProGRP quantification in a clinical relevant concentration range using LC–MS/MS and a comprehensive internal standard. J. Chromatogr. B. Analyt. Technol. Biomed. Life Sci. 877(13), 1359–1365 (2009).
  Medline CASGoogle Scholar
• 51. Halquist MS, Karnes HT. Quantification of alefacept, an immunosuppressive fusion protein in human plasma using a protein analogue internal standard, trypsin cleaved signature peptides and liquid chromatography tandem mass spectrometry. J. Chromatogr. B. Analyt. Technol. Biomed. Life Sci. 879(11-12), 789–798 (2011).
  Medline CASGoogle Scholar
• 52. Pan S, Aebersold R. Quantitative proteomics by stable isotope labeling and mass spectrometry. Methods Mol. Biol. 209–218 (2007).
  MedlineGoogle Scholar
• 53. Faria M, Halquist MS, Yuan M, Mylott W Jr, Jenkins RG, Karnes HT. Comparison of a stable isotope labeled (SIL) peptide and an extended SIL peptide as internal standards to track digestion variability of an unstable signature peptide during quantification of a cancer biomarker, human osteopontin, from plasma using capillary microflow LC–MS/MS. J. Chromatogr. B. Analyt. Technol. Biomed. Life Sci. 1001, 156–168 (2015).
  Medline CASGoogle Scholar
• 54. Faria M, Halquist MS, Yuan M, Mylott W Jr, Jenkins RG, Karnes HT. An extended stable isotope‐labeled signature peptide internal standard for tracking immunocapture of human plasma osteopontin for LC‐MS/MS quantification. Biomed. Chromatogr. 29(11), 1780–1782 (2015).
  Medline CASGoogle Scholar