51
Views
16
CrossRef citations to date
0
Altmetric
Review

Discovery of regulatory molecular events and biomarkers using 2D capillary chromatography and mass spectrometry

, &
Pages 63-74 | Published online: 09 Jan 2014

References

  • Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Seraphin B. A generic protein purification method for protein complex characterization and proteome exploration. Nature Biotechnol. 17, 1030–1032 (1999).
  • Sanders SL, Jennings J, Canutescu A, Link AJ, Weil PA. Proteomics of the eukaryotic transcription machinery: identification of proteins associated with components of yeast TFIID by multidimensional mass spectrometry. Mol. Cell Biol. 22, 4723–4738 (2002).
  • Link AJ, Fleischer TC, Weaver CM, Gerbasi VR, Jennings JL. Purifying protein complexes for mass spectrometry: applications to protein translation. Methods 35, 274–290 (2005).
  • Powell DW, Weaver CM, Jennings JL et al. Cluster analysis of mass spectrometry data reveals a novel component of SAGA. Mol. Cell Biol. 24, 7249–7259 (2004).
  • Duncan MW, Hunsucker SW. Proteomics as a tool for clinically relevant biomarker discovery and validation. Exp. Biol. Med. (Maywood) 230, 808–817 (2005).
  • Veenstra TD, Conrads TP, Hood BL, Avellino AM, Ellenbogen RG, Morrison RS. Biomarkers: mining the biofluid proteome. Mol. Cell. Proteomics 4, 409–418 (2005).
  • Link AJ, Eng J, Schieltz DM et al. Direct analysis of protein complexes using mass spectrometry. Nature Biotechnol. 17, 676–682 (1999).
  • Yates JR III, Eng JK, McCormack AL. Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. Anal. Chem. 67, 3202–3210 (1995).
  • Lominadze G, Powell DW, Luerman GC, Link AJ, Ward RA, McLeish KR. Proteomic analysis of human neutrophil granules. Mol. Cell. Proteomics 4, 1503–1521 (2005).
  • Yates JR III, Eng JK, McCormack AL, Schieltz D. Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal. Chem. 67, 1426–1436 (1995).
  • Nesvizhskii AI, Keller A, Kolker E, Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646–4658 (2003).
  • Clauser KR, Hall SC, Smith DM et al. Rapid mass spectrometric peptide sequencing and mass matching for characterization of human melanoma proteins isolated by two-dimensional PAGE. Proc. Natl Acad. Sci. USA 92, 5072–5076 (1995).
  • Craig R, Beavis RC. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20, 1466–1467 (2004).
  • Fenyo D, Beavis RC. A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal. Chem. 75, 768–774 (2003).
  • Gao J, Friedrichs MS, Dongre AR, Opiteck GJ. Guidelines for the routine application of the peptide hits technique. J. Am. Soc. Mass Spectrom. 16, 1231–1238 (2005).
  • Keller A, Nesvizhskii AI, Kolker E, Aebersold R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383–5392 (2002).
  • Tabb DL, McDonald WH, Yates JR III. DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J. Proteome Res. 1, 21–26 (2002).
  • Everley PA, Krijgsveld J, Zetter BR, Gygi SP. Quantitative cancer proteomics: stable isotope labeling with amino acids in cell culture (SILAC) as a tool for prostate cancer research. Mol. Cell. Proteomics 3, 729–735 (2004).
  • Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnol. 17, 994–999 (1999).
  • Ong SE, Blagoev B, Kratchmarova I et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1, 376–386 (2002).
  • Wang W, Zhou H, Lin H et al. Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal. Chem. 75, 4818–4826 (2003).
  • Wiener MC, Sachs JR, Deyanova EG, Yates NA. Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures. Anal. Chem. 76, 6085–6096 (2004).
  • Old WM, Meyer-Arendt K, Aveline-Wolf L et al. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol. Cell. Proteomics 4, 1487–14502 (2005).
  • Listgarten J, Emili A. Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteomics 4, 419–434 (2005).
  • Radulovic D, Jelveh S, Ryu S et al. Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteomics 3, 984–997 (2004).
  • Ho Y, Gruhler A, Heilbut A et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180–183 (2002).
  • Gavin AC, Bosche M, Krause R et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141–147 (2002).
  • Bouwmeester T, Bauch A, Ruffner H et al. A physical and functional map of the human TNF-α/NF-κ B signal transduction pathway. Nature Cell Biol. 6, 97–105 (2004).
  • Ficarro S, Chertihin O, Westbrook VA et al. Phosphoproteome analysis of capacitated human sperm. Evidence of tyrosine phosphorylation of a kinase-anchoring protein 3 and valosin-containing protein/p97 during capacitation. J. Biol. Chem. 278, 11579–11589 (2003).
  • Huh WK, Falvo JV, Gerke LC et al. Global analysis of protein localization in budding yeast. Nature 425, 686–691 (2003).
  • Ghaemmaghami S, Huh WK, Bower K et al. Global analysis of protein expression in yeast. Nature 425, 737–741 (2003).
  • Zhu H, Bilgin M, Bangham R et al. Global analysis of protein activities using proteome chips. Science 293, 2101–2105 (2001).
  • Harrison PM, Kumar A, Lang N, Snyder M, Gerstein M. A question of size: the eukaryotic proteome and the problems in defining it. Nucleic Acids Res. 30, 1083–1090 (2002).
  • Gould KL, Ren L, Feoktistova AS, Jennings JL, Link AJ. Tandem affinity purification and identification of protein complex components. Methods 33, 239–244 (2004).
  • Yoon HJ, Feoktistova A, Wolfe BA, Jennings JL, Link AJ, Gould KL. Proteomics analysis identifies new components of the fission and budding yeast anaphase-promoting complexes. Curr. Biol. 12, 2048–2054 (2002).
  • Venkatram S, Tasto JJ, Feoktistova A, Jennings JL, Link AJ, Gould KL. Identification and characterization of two novel proteins affecting fission yeast γ-tubulin complex function. Mol. Biol. Cell 15, 2287–2301 (2004).
  • Ohi MD, Link AJ, Ren L, Jennings JL, McDonald WH, Gould KL. Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNAs. Mol. Cell Biol. 22, 2011–2024 (2002).
  • Butland G, Peregrin-Alvarez JM, Li J et al. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433, 531–537 (2005).
  • Veraksa A, Bauer A, Artavanis-Tsakonas S. Analyzing protein complexes in Drosophila with tandem affinity purification-mass spectrometry. Dev. Dyn. 232, 827–834 (2005).
  • Rohila JS, Chen M, Cerny R, Fromm ME. Improved tandem affinity purification tag and methods for isolation of protein heterocomplexes from plants. Plant J. 38, 172–181 (2004).
  • Coulombe B, Jeronimo C, Langelier MF, Cojocaru M, Bergeron D. Interaction networks of the molecular machines that decode, replicate, and maintain the integrity of the human genome. Mol. Cell. Proteomics 3, 851–856 (2004).
  • Forler D, Kocher T, Rode M, Gentzel M, Izaurralde E, Wilm M. An efficient protein complex purification method for functional proteomics in higher eukaryotes. Nature Biotechnol. 21, 89–92 (2003).
  • Skill NJ, Johnson TS, Coutts IG et al. Inhibition of transglutaminase activity reduces extracellular matrix accumulation induced by high glucose levels in proximal tubular epithelial cells. J. Biol. Chem. 279, 47754–47762 (2004).
  • Haneda M, Koya D, Isono M, Kikkawa R. Overview of glucose signaling in mesangial cells in diabetic nephropathy. J. Am. Soc. Nephrol. 14, 1374–1382 (2003).
  • Lee KK, Florens L, Swanson SK, Washburn MP, Workman JL. The deubiquitylation activity of Ubp8 is dependent upon Sgf11 and its association with the SAGA complex. Mol. Cell Biol. 25, 1173–1182 (2005).
  • Adkins JN, Varnum SM, Auberry KJ et al. Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry. Mol. Cell. Proteomics 1, 947–955 (2002).
  • Gao J, Garulacan LA, Storm SM et al. Biomarker discovery in biological fluids. Methods 35, 291–302 (2005).
  • Jacobs JM, Adkins JN, Qian WJ et al. Utilizing human blood plasma for proteomic biomarker discovery. J. Proteome Res. 4, 1073–1085 (2005).
  • Tang HY, Ali-Khan N, Echan LA, Levenkova N, Rux JJ, Speicher DW. A novel four-dimensional strategy combining protein and peptide separation methods enables detection of low-abundance proteins in human plasma and serum proteomes. Proteomics 5, 3329–3342 (2005).
  • Peng J, Elias JE, Thoreen CC, Licklider LJ, Gygi SP. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J. Proteome Res. 2, 43–50 (2003).
  • Washburn MP, Wolters D, Yates JR III. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nature Biotechnol. 19, 242–247 (2001).
  • Wagner K, Miliotis T, Marko-Varga G, Bischoff R, Unger KK. An automated on-line multidimensional HPLC system for protein and peptide mapping with integrated sample preparation. Anal. Chem. 74, 809–820 (2002).
  • Issaq HJ, Chan KC, Janini GM, Muschik GM. A simple two-dimensional high performance liquid chromatography/high performance capillary electrophoresis set-up for the separation of complex mixtures. Electrophoresis 20, 1533–1537 (1999).
  • Opiteck GJ, Jorgenson JW. Two-dimensional SEC/RPLC coupled to mass spectrometry for the analysis of peptides. Anal. Chem. 69, 2283–2291 (1997).
  • Raida M, Schulz-Knappe P, Heine G, Forssmann WG. Liquid chromatography and electrospray mass spectrometric mapping of peptides from human plasma filtrate. J. Am. Soc. Mass Spectrom. 10, 45–54 (1999).
  • Zolotarjova N, Martosella J, Nicol G, Bailey J, Boyes BE, Barrett WC. Differences among techniques for high-abundant protein depletion. Proteomics 5, 3304–3313 (2005).
  • Zhou M, Lucas DA, Chan KC et al. An investigation into the human serum ‘interactome’. Electrophoresis 25, 1289–1298 (2004).
  • Zhang H, Yi EC, Li XJ et al. High throughput quantitative analysis of serum proteins using glycopeptide capture and liquid chromatography mass spectrometry. Mol. Cell. Proteomics 4, 144–155 (2005).
  • Chalmers MJ, Mackay CL, Hendrickson CL et al. Combined top-down and bottom-up mass spectrometric approach to characterization of biomarkers for renal disease. Anal. Chem. 77, 7163–7171 (2005).
  • Davis MT, Spahr CS, McGinley MD et al. Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry. II. Limitations of complex mixture analyses. Proteomics 1, 108–117 (2001).
  • Hewitt SM, Dear J, Star RA. Discovery of protein biomarkers for renal diseases. J. Am. Soc. Nephrol. 15, 1677–1689 (2004).
  • Pang JX, Ginanni N, Dongre AR, Hefta SA, Opitek GJ. Biomarker discovery in urine by proteomics. J. Proteome Res. 1, 161–169 (2002).
  • Spahr CS, Davis MT, McGinley MD et al. Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry. I. Profiling an unfractionated tryptic digest. Proteomics 1, 93–107 (2001).
  • Sun W, Li F, Wu S et al. Human urine proteome analysis by three separation approaches. Proteomics 5, 4994–5001 (2005).
  • Wang L, Li F, Sun W et al. Concanavalin A captured glycoproteins in healthy human urine. Mol. Cell. Proteomics (2005) (In Press).
  • Clavant SP, Greive KA, Nikolovski J, Reeve S, Smith AI, Comper WD. Albumin fragments in normal rat urine are derived from rapidly degraded filtered albumin. Nephrology (Carlton) 8, 72–79 (2003).
  • Hoorn EJ, Pisitkun T, Zietse R et al. Prospects for urinary proteomics: exosomes as a source of urinary biomarkers. Nephrology (Carlton) 10, 283–290 (2005).
  • Pisitkun T, Shen RF, Knepper MA. Identification and proteomic profiling of exosomes in human urine. Proc. Natl Acad. Sci. USA 101, 13368–13373 (2004).
  • Keay SK, Szekely Z, Conrads TP et al. An antiproliferative factor from interstitial cystitis patients is a frizzled 8 protein-related sialoglycopeptide. Proc. Natl Acad. Sci. USA 101, 11803–11808 (2004).
  • Wittke S, Fliser D, Haubitz M et al. Determination of peptides and proteins in human urine with capillary electrophoresis-mass spectrometry, a suitable tool for the establishment of new diagnostic markers. J. Chromatogr. A 1013, 173–181 (2003).
  • Perkins DN, Pappin DJ, Creasy DM, Cottrell JS. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551–3567 (1999).
  • Han DK, Eng J, Zhou H, Aebersold R. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nature Biotechnol. 19, 946–951 (2001).
  • Resing KA, Meyer-Arendt K, Mendoza AM et al. Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics. Anal. Chem. 76, 3556–3568 (2004).
  • Sadygov RG, Liu H, Yates JR. Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases. Anal. Chem. 76, 1664–1671 (2004).
  • Quackenbush J. Computational analysis of microarray data. Nature Rev. Genet. 2, 418–427 (2001).
  • Munchbach M, Quadroni M, Miotto G, James P. Quantitation and facilitated de novo sequencing of proteins by isotopic N-terminal labeling of peptides with a fragmentation-directing moiety. Anal. Chem. 72, 4047–4057 (2000).
  • Ross PL, Huang YN, Marchese JN et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3, 1154–1169 (2004).
  • Washburn MP, Ulaszek RR, Yates JR III. Reproducibility of quantitative proteomic analyses of complex biological mixtures by multidimensional protein identification technology. Anal. Chem. 75, 5054–5061 (2003).
  • Yao X, Freas A, Ramirez J, Demirev PA, Fenselau C. Proteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal. Chem. 73, 2836–2842 (2001).
  • Zhou H, Ranish JA, Watts JD, Aebersold R. Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nature Biotechnol. 20, 512–515 (2002).
  • Yi EC, Li XJ, Cooke K et al. Increased quantitative proteome coverage with 13C/12C-based, acid-cleavable isotope-coded affinity tag reagent and modified data acquisition scheme. Proteomics 5, 380–387 (2005).
  • Gao J, Opiteck GJ, Friedrichs MS, Dongre AR, Hefta SA. Changes in the protein expression of yeast as a function of carbon source. J. Proteome Res. 2, 643–649 (2003).
  • Liu H, Sadygov RG, Yates JR III. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 76, 4193–4201 (2004).

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.