Isobaric protein and peptide quantification: perspectives and issues

References

• Yates JR, Ruse CI, Nakorchevsky A. Proteomics by mass spectrometry: approaches, advances, and applications. Annu. Rev. Biomed. Eng.11, 49–79 (2009).
   PubMed Web of Science ®Google Scholar
• Bachi A, Bonaldi T. Quantitative proteomics as a new piece of the systems biology puzzle. J. Proteomics71(3), 357–367 (2008).
   PubMed Web of Science ®Google Scholar
• Vandenbogaert M, Li-Thiao-Te S, Kaltenbach HM et al. Alignment of LC-MS images, with applications to biomarker discovery and protein identification. Proteomics8(4), 650–672 (2008).
   PubMed Web of Science ®Google Scholar
• Mueller LN, Brusniak MY, Mani DR, Aebersold R. An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J. Proteome Res.7(1), 51–61 (2008).
   PubMed Web of Science ®Google Scholar
• Gygi SP, Rist B, Gerber SA et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol.17(10), 994–999 (1999).
   PubMed Web of Science ®Google Scholar
• Schmidt A, Kellermann J, Lottspeich F. A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics5(1), 4–15 (2005).
   PubMed Web of Science ®Google Scholar
• Chakraborty A, Regnier FE. Global internal standard technology for comparative proteomics. J. Chromatogr. A949(1–2), 173–184 (2002).
   PubMed Web of Science ®Google Scholar
• Thompson A, Schafer J, Kuhn K et al. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem.75(8), 1895–1904 (2003).
   PubMed Web of Science ®Google Scholar
• Ross PL, Huang YN, Marchese JN et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell Proteomics3(12), 1154–1169 (2004).
   PubMed Web of Science ®Google Scholar
• Wiese S, Reidegeld KA, Meyer HE, Warscheid B. Protein labeling by iTRAQ: a new tool for quantitative mass spectrometry in proteome research. Proteomics7(3), 340–350 (2007).
   PubMed Web of Science ®Google Scholar
• Engmann O, Campbell J, Ward M, Giese KP, Thompson AJ. Comparison of a protein-level and peptide-level labeling strategy for quantitative proteomics of synaptosomes using isobaric tags. J. Proteome Res.9(5), 2725–2733 (2010).
   PubMed Web of Science ®Google Scholar
• Li S, Zeng D. CILAT – a new reagent for quantitative proteomics. Chem. Commun. (Camb.)21, 2181–2183 (2007).
   PubMedGoogle Scholar
• Zeng D, Li S. Improved CILAT reagents for quantitative proteomics. Bioorg. Med. Chem. Lett.19(7), 2059–2061 (2009).
   PubMed Web of Science ®Google Scholar
• Xiang F, Ye H, Chen R, Fu Q, Li L. N,N-dimethyl leucines as novel isobaric tandem mass tags for quantitative proteomics and peptidomics. Anal. Chem.82(7), 2817–2825 (2010).
   PubMed Web of Science ®Google Scholar
• Koehler CJ, Strozynski M, Kozielski F, Treumann A, Thiede B. Isobaric peptide termini labeling for MS/MS-based quantitative proteomics. J. Proteome Res.8(9), 4333–4341 (2009).
   PubMed Web of Science ®Google Scholar
• Cunningham C Jr, Glish GL, Burinsky DJ. High amplitude short time excitation: a method to form and detect low mass product ions in a quadrupole ion trap mass spectrometer. J. Am. Soc. Mass Spectrom.17(1), 81–84 (2006).
   PubMed Web of Science ®Google Scholar
• Han H, Pappin DJ, Ross PL, McLuckey SA. Electron transfer dissociation of iTRAQ labeled peptide ions. J. Proteome Res.7(9), 3643–3648 (2008).
   PubMed Web of Science ®Google Scholar
• Phanstiel D, Zhang Y, Marto JA, Coon JJ. Peptide and protein quantification using iTRAQ with electron transfer dissociation. J. Am. Soc. Mass Spectrom.19(9), 1255–1262 (2008).
   PubMed Web of Science ®Google Scholar
• Phanstiel D, Unwin R, McAlister GC, Coon JJ. Peptide quantification using 8-plex isobaric tags and electron transfer dissociation tandem mass spectrometry. Anal. Chem.81(4), 1693–1698 (2009).
   PubMed Web of Science ®Google Scholar
• Viner RI, Zhang T, Second T, Zabrouskov V. Quantification of post-translationally modified peptides of bovine a-crystallin using tandem mass tags and electron transfer dissociation. J. Proteomics72(5), 874–885 (2009).
   PubMed Web of Science ®Google Scholar
• Griffin TJ, Xie H, Bandhakavi S et al. iTRAQ reagent-based quantitative proteomic analysis on a linear ion trap mass spectrometer. J. Proteome Res.6(11), 4200–4209 (2007).
   PubMed Web of Science ®Google Scholar
• Bantscheff M, Boesche M, Eberhard D et al. Robust and sensitive iTRAQ quantification on an LTQ Orbitrap mass spectrometer. Mol. Cell Proteomics7(9), 1702–1713 (2008).
   PubMed Web of Science ®Google Scholar
• Guo T, Gan CS, Zhang H et al. Hybridization of pulsed-Q dissociation and collision-activated dissociation in linear ion trap mass spectrometer for iTRAQ quantitation. J. Proteome Res.7(11), 4831–4840 (2008).
   PubMed Web of Science ®Google Scholar
• Boja ES, Phillips D, French SA, Harris RA, Balaban RS. Quantitative mitochondrial phosphoproteomics using iTRAQ on an LTQ-Orbitrap with high energy collision dissociation. J. Proteome Res.8(10), 4665–4675 (2009).
   PubMed Web of Science ®Google Scholar
• Olsen JV, Macek B, Lange O et al. Higher-energy C-trap dissociation for peptide modification analysis. Nat. Methods4(9), 709–712 (2007).
   PubMed Web of Science ®Google Scholar
• Kocher T, Pichler P, Schutzbier M et al. High precision quantitative proteomics using iTRAQ on an LTQ Orbitrap: a new mass spectrometric method combining the benefits of all. J. Proteome Res.8(10), 4743–4752 (2009).
   PubMed Web of Science ®Google Scholar
• Mikesh LM, Ueberheide B, Chi A et al. The utility of ETD mass spectrometry in proteomic analysis. Biochim. Biophys. Acta1764(12), 1811–1822 (2006).
   PubMed Web of Science ®Google Scholar
• Ow SY, Salim M, Noirel J et al. iTRAQ underestimation in simple and complex mixtures: ‘the good, the bad and the ugly’. J. Proteome Res.8(11), 5347–5355 (2009).
   PubMed Web of Science ®Google Scholar
• Lacerda CM, Xin L, Rogers I, Reardon KF. Analysis of iTRAQ data using Mascot and Peaks quantification algorithms. Brief Funct. Genomic Proteomic7(2), 119–126 (2008).
   PubMedGoogle Scholar
• D’Ascenzo M, Choe L, Lee KH. iTRAQPak: an R based analysis and visualization package for 8-plex isobaric protein expression data. Brief Funct. Genomic Proteomic7(2), 127–135 (2008).
   PubMedGoogle Scholar