Protein primary structure using orthogonal fragmentation techniques in Fourier transform mass spectrometry

References

• Link AJ, Eng J, Schieltz DM et al. Direct analysis of protein complexes using mass spectrometry.Nature Biotechnol.17, 676–682 (1999).
   PubMed Web of Science ®Google Scholar
• Pandey A, Mann M. Proteomics to study genes and genomes.Nature405, 837–846 (2000).
   PubMed Web of Science ®Google Scholar
• Aebersold R, Mann M. Mass spectrometry-based proteomics.Nature422, 198–207 (2003).
   PubMed Web of Science ®Google Scholar
• Perkins DN, Pappin DJ, Creasy DM, Cottrell JS. Probability-based protein identification by searching sequence databases using mass spectrometry data.Electrophoresis20, 3551–3567 (1999).
   PubMed Web of Science ®Google Scholar
• Eng JK, McCormack AL, Yates JR III. An approach to correlate tandem mass-spectral data of peptides with amino-acid-sequences in a protein database.J. Am. Soc. Mass Spectrom.5,976–989 (1994).
   PubMed Web of Science ®Google Scholar
• Bruce J, Anderson GA, Wen J, Harkewicz R, Smith RD. High mass measurement accuracy for 100% sequence coverage of enzymatically digested bovine serum albumin from an ESI-FTICR mass spectrum.Anal. Chem.71, 2595–2599 (1999).
   PubMed Web of Science ®Google Scholar
• Palmblad M, Wetterhall M, Markides K, Håkansson P, Bergquist J. Analysis of enzymatically digested proteins and protein mixtures using a 9.4 Tesla Fourier transform.Rapid Commun. Mass Spectrom.12, 1029–1034 (2000).
   Google Scholar
• Olsen JV, Mann M. Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation.Proc. Natl Acad. Sci. USA101, 13417–13422 (2004).
   PubMed Web of Science ®Google Scholar
• Gibson BW, Biemann K. Strategy for the mass spectrometric verification and correction of the primary structures of proteins deduced from their DNA sequences.Proc. Natl Acad. Sci. USA81, 1956–1960 (1984).
   PubMed Web of Science ®Google Scholar
• Zubarev RA, Håkansson P, Sundqvist BUR. Accurate monoisotopic mass measurements of peptides: possibilities and limitations of high resolution time-of-flight particle desorption mass spectrometry.Rapid Commun. Mass Spectrom.10, 1386–1392 (1996).
   Web of Science ®Google Scholar
• Spengler B. De novo sequencing, peptide composition analysis, and composition-based sequencing: a new strategy employing accurate mass determination by fourier transform ion cyclotron resonance mass spectrometry.J. Am. Soc. Mass Spectrom.15, 703–714 (2004).
   PubMed Web of Science ®Google Scholar
• Conrads TP, Anderson GA, Veenstra TD, Paša-Tolic L, Smith RD. Utility of accurate mass tags for proteome-wide protein identification.Anal. Chem.72, 3349–3354 (2000).
   PubMed Web of Science ®Google Scholar
• Smith RD, Anderson GA, Lipton MS et al. An accurate mass tag strategy for quantitative and high-throughput proteome measurements.Proteomics2, 513–523 (2002).
   PubMed Web of Science ®Google Scholar
• Carr S, Aebersold R, Baldwin M, Burlingame A, Clauser K, Nesvizhskii A. The need for guidelines in publication of peptide and protein identification data.Mol. Cell. Proteomics3, 531–522 (2004).
   PubMed Web of Science ®Google Scholar
• Rush J, Moritz A, Lee KA et al. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells.Nature Biotechnol.23, 94–101 (2004).
   PubMed Web of Science ®Google Scholar
• Bern M, Goldberg D, McDonald WH, Yates JR III. Automatic quality assessment of peptide tandem mass spectra.Bioinformatics20, 49–54 (2004).
   PubMed Web of Science ®Google Scholar
• Mann M, Wilm M. Error-tolerant identification of peptides in sequence databases by peptide sequence tags.Anal. Chem.66, 4390–4399 (1994).
   PubMed Web of Science ®Google Scholar
• Dongre AR, Somogyi A, Wysocki VH. Surface-induced dissociation: an effective tool to probe structure, energetics and fragmentation mechanisms of protonated peptides.J. Mass Spectrom.31, 339–350 (1996).
   PubMed Web of Science ®Google Scholar
• Nielsen ML, Savitski MM, Zubarev RA. Improving protein identification using complementary fragmentation techniques in Fourier transform mass spectrometry.Mol. Cell. Proteomics4, 835–845 (2005).
   PubMed Web of Science ®Google Scholar
• Rodriquez CF, Cunje A, Shoeib T, Chu IK, Hopkinson AC, Siu KWM. Proton migration and tautomerism in protonated triglycine.J. Am. Chem. Soc.123, 3006–3012 (2001).
   PubMed Web of Science ®Google Scholar
• Yu W, Vath JE, Huberty MC, Martin SA. Identification of the facile gas-phase cleavage of the Asp-Pro and Asp-Xxx peptide bonds in matrix-assisted laser-desorption time-of-flight mass spectrometry.Anal. Chem.65, 3015–3023 (1993).
   PubMed Web of Science ®Google Scholar
• Huang Y, Triscari JM, Wysocki VH et al. Dissociation behaviors of doubly-charged tryptic peptides: correlation of gas-phase cleavage abundance with ramachandran plots.J. Am. Chem. Soc.,126, 3034–3035 (2004).
   PubMed Web of Science ®Google Scholar
• Huang Y, Triscari JM, Tseng GC et al. Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns.Anal. Chem.77, 5800–5813 (2005).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• Savitski MM, Nielsen ML, Zubarev RA. New database-independent, sequence-tag-based scoring of peptide MS/MS data validates Mowse scores, recovers below-threshold data, singles out modified peptides and assesses the quality of MS/MS techniques.Mol. Cell. Proteomics4, 1180–1188 (2005).
   PubMed Web of Science ®Google Scholar
• Mann M, Wilm M. Error-tolerant identification of peptides in sequence databases by peptide sequence tags.Anal. Chem.66, 4390–4399 (1994).
   PubMed Web of Science ®Google Scholar
• Savitski MM, Nielsen ML, Kjeldsen F, Zubarev RA. Proteomics-grade de novo sequencing approach.J. Proteome Res.4, 2348–2354 (2005).
   PubMed Web of Science ®Google Scholar
• Budnik BA, Nielsen ML, Olsen JV et al. Can relative cleavage frequencies in peptides provide additional sequence information?Int. J. Mass Spectrom.219, 283–294 (2002).
   Web of Science ®Google Scholar
• Tang XJ, Thibault P, Boyd RK. Fragmentation reactions of multiply-protonated peptides and implications for sequencing by tandem mass spectrometry with low-energy collision-induced dissociation. Anal. Chem.65, 2824–2834 (1993).
   PubMed Web of Science ®Google Scholar
• Zhang Z, McElvain JS. De novo peptide sequencing by two-dimensional fragment correlation mass spectrometry.Anal. Chem.72, 2337–2350 (2000).
   PubMed Web of Science ®Google Scholar
• Olsen JV, Mann M. Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation.Proc. Natl Acad. Sci. USA101, 13417–13422 (2004).
   PubMed Web of Science ®Google Scholar
• Thompson MS, Cui W, Reilly JP. Fragmentation of singly charged peptide ions by photodissociation at λ=157 nm.Angew. Chem. Int. Ed.43, 4791–4794 (2004).
   PubMed Web of Science ®Google Scholar
• Zubarev RA, Kelleher NL, McLafferty FW. Electron capture dissociation of multiply charged protein cations. A non-ergodic process.J. Am. Chem. Soc.120, 3265–3266 (1998).
   Web of Science ®Google Scholar
• Zubarev RA, Kruger NA, Fridriksson EK et al. Electron capture dissociation of gaseous multiply-charged proteins is favored at disulfide bonds and other sites of high hydrogen atom affinity.J. Am. Chem. Soc.121, 2857–2862 (1999).
   Web of Science ®Google Scholar
• Zubarev RA. Electron capture dissociation tandem mass spectrometry.Curr. Opin. Biotechnol.15, 12–16 (2004).
   PubMed Web of Science ®Google Scholar
• Baba T, Hashimoto Y, Hasegawa H, Hirabayashi A, Waki I. Electron capture dissociation in a radio frequency ion trap. Anal. Chem.76, 4263–4266 (2004).
   PubMed Web of Science ®Google Scholar
• Silivra OA, Kjeldsen F, Ivonin IA, Zubarev RA. Electron capture dissociation in a quadrupole ion trap: first results.J. Am. Soc. Mass Spectrom.16, 22–27 (2005).
   PubMed Web of Science ®Google Scholar
• Syka JEP, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry.Proc. Natl Acad. Sci. USA101, 9528–9533 (2004).
   PubMed Web of Science ®Google Scholar
• Horn DM, Zubarev RA, McLafferty FW. Automated de novo sequencing of proteins by tandem high-resolution mass spectrometry. Proc. Natl Acad. Sci USA97, 10313–10317 (2000).
   PubMed Web of Science ®Google Scholar
• Grossmann J, Roos FF, Cieliebak M et al. Audens: a tool for automated peptide de novo sequencing. J. Proteome Res.10, 1768–1774 (2005).
   Google Scholar
• Sze SK, Ge Y, Oh HB, McLafferty FW. Plasma electron capture dissociation for the characterization of large proteins by top down mass spectrometry. Anal. Chem.75, 1599–1603 (2003).
   PubMed Web of Science ®Google Scholar
• Horn DM, Ge Y, McLafferty FW. Activated ion electron capture dissociation for mass spectral sequencing of larger (42 kDa) proteins. Anal. Chem.72, 4778–4784 (2000).
   PubMed Web of Science ®Google Scholar
• Horn DM, Zubarev RA, McLafferty FW. Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules.J. Am. Soc. Mass Spectrom.11, 320–332 (2000).
   PubMed Web of Science ®Google Scholar
• Taylor GK, Kim YB, Forbes AJ, Meng FY, McCarthy R, Kelleher NL. Web and database software for identification of intact proteins using “top down” mass spectrometry. Anal. Chem.75, 4081–4086 (2003).
   PubMed Web of Science ®Google Scholar
• Kjeldsen F, Zubarev RA. Secondary losses via γ-lactam formation in hot electron capture dissociation: a missing link to complete de novo sequencing of proteins? J. Am. Chem. Soc.125, 6628–6629 (2003).
   PubMed Web of Science ®Google Scholar
• Cooper HJ, Hakansson K, Marshall AG. The role of electron capture dissociation in biomolecular analysis. Mass Spectrom. Rev. 24, 201–222 (2005).
   Google Scholar
• Kjeldsen F, Haselmann KF, Budnik BA, Sørensen ES, Zubarev RA. Complete characterisation of post-translational modification sites in the bovine milk protein PP3 by tandem mass spectrometry with electron capture dissociation as the last stage. Anal. Chem.75, 2355–2361 (2003).
   PubMed Web of Science ®Google Scholar
• Kjeldsen F, Sørensen E, Zubarev RA. Distinguishing of Ile/Leu amino acid residues in the PP3 protein by (hot) electron capture dissociation in Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem.75, 1267–1274 (2003).
   PubMed Web of Science ®Google Scholar
• Kjeldsen F, Budnik BA, Haselmann KF, Jensen F, Zubarev RA. Dissociative capture of hot (3–13 eV) electrons by polypeptide polycations: an efficient process accompanied by secondary fragmentation. Chem. Phys. Lett.356, 201–206 (2002).
   Web of Science ®Google Scholar
• Artigues A, Birkett A, Schirch V. Evidence for the in vivo deamidation and isomerization of an asparaginyl residue in cytosolic serine hydroxymethyltransferase. J. Biol. Chem.265, 4853–4858 (1990).
   PubMed Web of Science ®Google Scholar
• Cournoyer JJ, Pittman JJ, Ivleva VB et al. Deamidation: differentiation of aspartyl from isoaspartyl products in peptides. Prot. Sci.14, 452–563 (2005).
   PubMed Web of Science ®Google Scholar
• Adams C, Budnik BA, Haselmann KF, Kjeldsen F, Zubarev RA. Electron capture dissociation distinguishes a single D-amino acid in a protein and probes the tertiary structure.J. Am. Soc. Mass Spectrom.15, 1087–1098 (2004).
   PubMed Web of Science ®Google Scholar
• Adams C, Zubarev RA. Distinguishing and quantification of peptides and proteins containing D-amino acids by tandem mass spectrometry. Anal. Chem.77, 4571–4580 (2005).
   PubMed Web of Science ®Google Scholar
• Budnik BA, Haselmann KF, Zubarev RA. Electron detachment dissociation of peptide di-anions: an electron-hole recombination phenomenon.Chem. Phys. Lett.342, 299–302 (2001).
   Web of Science ®Google Scholar
• Kjeldsen F, Silivra OA, Ivonin IA, Haselmann KF, Gorshkov M, Zubarev RA. Cα-C backbone fragmentation dominates in electron detachment dissociation of gas-phase poly-peptide anions. Chemistry11, 1803–1812 (2005).
   PubMed Web of Science ®Google Scholar
• Johnson JR, Meng FY, Forbes AJ, Cargile BJ, Kelleher NL. Fourier-transform mass spectrometry for automated fragmentation and identification of 5–20 kDa proteins in mixtures.Electrophoresis23, 3217–3223 (2002).
   PubMed Web of Science ®Google Scholar