75
Views
30
CrossRef citations to date
0
Altmetric
Perspective

Electron capture dissociation in the analysis of protein phosphorylation

&
Pages 149-159 | Published online: 09 Jan 2014

References

  • Pawson T, Scott JD. Protein phosphorylation in signaling – 50 years and counting. Trends Biochem. Sci.30(6), 286–290 (2005).
  • Hunter T. Protein kinases and phosphatases – the yin and yang of protein phosphorylation and signaling. Cell80(2), 225–236 (1995).
  • Cohen PTW. Novel protein serine/threonine phosphatases: variety is the spice of life. Trends Biochem. Sci.22(7), 245–251 (1997).
  • Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S. The protein kinase complement of the human genome. Science298(5600), 1912–1934 (2002).
  • Sickmann A, Meyer HE. Phosphoamino acid analysis. Proteomics1(2), 200–206 (2001).
  • Hunter T, Sefton BM. Transforming gene product of Rous sarcoma virus phosphorylates tyrosine. Proc. Natl Acad. Sci. USA77(3), 1311–1315 (1980).
  • Loyet KM, Stults JT, Arnott D. Mass spectrometric contributions to the practice of phosphorylation site mapping through 2003: a literature review. Mol. Cell. Proteomics4(3), 235–245 (2005).
  • Mann M, Ong SE, Gronborg M et al. Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends Biotech.20(6), 261–268 (2002).
  • Wu S-L, Kim J, Bandle RW et al. Dynamic profiling of the post-translational modifications and interaction partners of epidermal growth factor receptor signaling after stimulation by epidermal growth factor using extended range proteomic analysis (ERPA). Mol. Cell. Proteomics5(9), 1610–1627 (2006).
  • de Godoy L, Olsen J, de Souza G et al. Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biol.7(6), R50 (2006).
  • Pinkse MWH, Uitto PM, Hilhorst MJ, Ooms B, Heck AJR. Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-nanoLC-ESI-MS/MS and titanium oxide precolumns. Anal. Chem.76(14), 3935–3943 (2004).
  • Ficarro SB, McCleland ML, Stukenberg PT et al. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol.20(3), 301–305 (2002).
  • Larsen MR, Thingholm TE, Jensen ON, Roepstorff P, Jorgensen TJD. Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol. Cell. Proteomics4(7), 873–886 (2005).
  • Beausoleil SA, Jedrychowski M, Schwartz D et al. Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc. Natl Acad. Sci. USA101(33), 12130–12135 (2004).
  • Nühse TS, Stensballe A, Jensen ON, Peck SC. Large-scale analysis of in vivo phosphorylated membrane proteins by immobilized metal ion affinity chromatography and mass spectrometry. Mol. Cell. Proteomics2(11), 1234–1243 (2003).
  • Steen H, Mann M. The ABC’s (and XYZ’s) of peptide sequencing. Nat. Rev. Mol. Cell Biol.5(9), 699–711 (2004).
  • Hunter AP, Games DE. Chromatographic and mass spectrometric methods for the identification of phosphorylation sites in phosphoproteins. Rapid Commun. Mass Spectrom.8(7), 559–570 (1994).
  • Cao P, Stults JT. Mapping the phosphorylation sites of proteins using on-line immobilized metal affinity chromatography/capillary electrophoresis/electrospray ionization multiple stage tandem mass spectrometry. Rapid Commun. Mass Spectrom.14(17), 1600–1606 (2000).
  • Gruhler A, Olsen JV, Mohammed S et al. Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol. Cell. Proteomics4(3), 310–327 (2005).
  • Li X, Gerber SA, Rudner AD et al. Large-scale phosphorylation analysis of α-factor-arrested Saccharomyces cerevisiae.J. Proteome Res.6(3), 1190–1197(2007).
  • Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat. Biotech.24(10), 1285–1292 (2006).
  • Schroeder MJ, Shabanowitz J, Schwartz JC, Hunt DF, Coon JJ. A neutral loss activation method for improved phosphopeptide sequence analysis by quadrupole ion trap mass spectrometry. Anal. Chem.76(13), 3590–3598 (2004).
  • Olsen JV, Blagoev B, Gnad F et al. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell127(3), 635–648 (2006).
  • Zubarev RA, Kelleher NL, McLafferty FW. Electron capture dissociation of multiply charged protein cations. A nonergodic process. J. Am. Chem. Soc.120(13), 3265–3266 (1998).
  • Savitski MM, Nielsen ML, Zubarev RA. Side-chain losses in electron capture dissociation to improve peptide identification. Anal. Chem.79(6), 2296–2302 (2007).
  • Cooper HJ. Investigation of the presence of b ions in electron capture dissociation mass spectra. J. Am. Soc. Mass Spectrom.16(12), 1932–1940 (2005).
  • Cooper HJ, Håkansson K, Marshall AG. The role of electron capture dissociation in biomolecular analysis. Mass Spectrom. Rev.24(2), 201–222 (2005).
  • Gorshkov MV, Masselon CD, Nikolaev EN et al. Considerations for electron capture dissociation efficiency in FTICR mass spectrometry. Int. J. Mass Spectrom.234(1–3), 131–136 (2004).
  • Zubarev RA, Horn DM, Fridriksson EK et al. Electron capture dissociation for structural characterization of multiply charged protein cations. Anal. Chem.72(3), 563–573 (2000).
  • Tsybin Y, Håkansson P, Budnik BA et al. Improved low-energy electron injection systems for high rate electron capture dissociation in Fourier transform ion cyclotron resonance mass spectrometry. Rapid Commun. Mass Spectrom.15(19), 1849–1854 (2001).
  • Tsybin YO, Hendrickson CL, Beu SC, Marshall AG. Impact of ion magnetron motion on electron capture dissociation Fourier transform ion cyclotron resonance mass spectrometry. Int. J. Mass Spectrom.255–256, 144–149 (2006).
  • Hakansson K, Chalmers MJ, Quinn JP et al. Combined electron capture and infrared multiphoton dissociation for multistage MS/MS in a Fourier transform ion cyclotron resonance mass spectrometer. Anal. Chem.75(13), 3256–3262 (2003).
  • Shi SDH, Hemling ME, Carr SA et al. Phosphopeptide/phosphoprotein mapping by electron capture dissociation mass spectrometry. Anal. Chem.73(1), 19–22 (2001).
  • Chalmers MJ, Hakansson K, Johnson R et al. Protein kinase A phosphorylation characterized by tandem Fourier transform ion cyclotron resonance mass spectrometry. Proteomics4(4), 970–981 (2004).
  • Horn DM, Ge Y, McLafferty FW. Activated ion electron capture dissociation for mass spectral sequencing of larger (42 kDa) proteins. Anal. Chem.72(20), 4778–4784 (2000).
  • Tsybin YO, Hakansson P, Wetterhall M, Markides KE, Bergquist J. Capillary electrophoresis and electron capture dissociation Fourier transform ion cyclotron resonance mass spectrometry for peptide mixture and protein digest analysis. Eur. J. Mass Spectrom.8(5), 389–395 (2002).
  • Palmblad M, Tsybin YO, Ramstrom M, Bergquist J, Hakansson P. Liquid chromatography and electron-capture dissociation in Fourier transform ion cyclotron resonance mass spectrometry. Rapid Commun. Mass Spectrom.16(10), 988–992 (2002).
  • Davidson W, Frego L. Micro-high-performance liquid chromatography/Fourier transform mass spectrometry with electron-capture dissociation for the analysis of protein enzymatic digests. Rapid Commun. Mass Spectrom.16(10), 993–998 (2002).
  • Cooper HJ, Akbarzadeh S, Heath JK, Zeller M. Data-dependent electron capture dissociation FT-ICR mass spectrometry for proteomic analyses. J. Proteome Res.4(5), 1538–1544 (2005).
  • Nielsen ML, Savitski MM, Zubarev RA. Improving protein identification using complementary fragmentation techniques in Fourier transform mass spectrometry. Mol. Cell. Proteomics4(6), 835–845 (2005).
  • Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl Acad. Sci. USA101(26), 9528–9533 (2004).
  • Swaney DL, McAlister GC, Wirtala M et al. Supplemental activation method for high-efficiency electron-transfer dissociation of doubly protonated peptide precursors. Anal. Chem.79(2), 477–485 (2007).
  • Molina H, Horn DM, Tang N, Mathivanan S, Pandey A. Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc. Natl Acad. Sci. USA104(7), 2199–2204 (2007).
  • Chi A, Huttenhower C, Geer LY et al. Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc. Natl Acad. Sci. USA104(7), 2193–2198 (2007).
  • Kelleher RL, Zubarev RA, Bush K et al. Localization of labile posttranslational modifications by electron capture dissociation: The case of γ-carboxyglutamic acid. Anal. Chem.71(19), 4250–4253 (1999).
  • Mirgorodskaya E, Roepstorff P, Zubarev RA. Localization of O-glycosylation sites in peptides by electron capture dissociation in a Fourier transform mass spectrometer. Anal. Chem.71(20), 4431–4436 (1999).
  • Hakansson K, Cooper HJ, Emmett MR et al. Electron capture dissociation and infrared multiphoton dissociation MS/MS of an N-glycosylated tryptic peptide to yield complementary sequence information. Anal. Chem.73(18), 4530–4536 (2001).
  • Stensballe A, Jensen ON, Olsen JV, Haselmann KF, Zubarev RA. Electron capture dissociation of singly and multiply phosphorylated peptides. Rapid Commun. Mass Spectrom.14(19), 1793–1800 (2000).
  • Kruger NA, Zubarev RA, Horn DM, McLafferty FW. Electron capture dissociation of multiply charged peptide cations. Int. J. Mass Spectrom.185–187, 787–793 (1999).
  • Creese AJ, Cooper HJ. Liquid chromatography electron capture dissociation tandem mass spectrometry (LC-ECD-MS/MS) versus liquid chromatography collision-induced dissociation tandem mass spectrometry (LC-CID MS/MS) for the identification of proteins. J. Am. Soc. Mass Spectrom. (2007) (Epub ahead of print).
  • Cooper HJ, Hudgins RR, Hakansson K, Marshall AG. Secondary fragmentation of linear peptides in electron capture dissociation. Int. J. Mass Spectrom.228(2–3), 723–728 (2003).
  • Sweet SMM, Creese AJ, Cooper HJ. Strategy for the identification of sites of phosphorylation in proteins: neutral loss triggered electron capture dissociation. Anal. Chem.78(21), 7563–7569 (2006).
  • Dongre AR, Jones JL, Somogyi A, Wysocki VH. Influence of peptide composition, gas-phase basicity, and chemical modification on fragmentation efficiency: evidence for the mobile proton model. J. Am. Chem. Soc.118(35), 8365–8374 (1996).
  • Patriksson A, Adams C, Kjeldsen F et al. Prediction of N–C-α bond cleavage frequencies in electron capture dissociation of Trp-cage dications by force-field molecular dynamics simulations. Int. J. Mass Spectrom.248(3), 124–135 (2006).
  • Budnik BA, Nielsen ML, Olsen JV et al. Can relative cleavage frequencies in peptides provide additional sequence information? Int. J. Mass Spectrom.219(1), 283–294 (2002).
  • Savitski MM, Kjeldsen F, Nielsen ML, Zubarev RA. Complementary sequence preferences of electron-capture dissociation and vibrational excitation in fragmentation of polypeptide polycations. Angew. Chem. Int. Ed. Engl. Engl.45(32), 5301–5303 (2006).
  • Syrstad EA, Turecek F. Toward a general mechanism of electron capture dissociation. J. Am. Soc. Mass Spectrom.16(2), 208–224 (2005).
  • Zubarev R. Protein primary structure using orthogonal fragmentation techniques in Fourier transform mass spectrometry. Exp. Rev. Proteomics3(2), 251–261 (2006).
  • Stingl C, Ihling C, Ammerer G, Sinz A, Mechtler K. Application of different fragmentation techniques for the analysis of phosphopeptides using a hybrid linear ion trap-FTICR mass spectrometer. Biochim. Biophys. Acta1764(12), 1842–1852 (2006).
  • Marshall AG. Accurate mass measurement: taking full advantage of nature’s isotopic complexity. Phys. Rev. B Condens. Matter346–347, 503–508 (2004).
  • Horn DM, Zubarev RA, McLafferty FW. Automated de novo sequencing of proteins by tandem high-resolution mass spectrometry. Proc. Natl Acad. Sci. USA97(19), 10313–10317 (2000).
  • Savitski MM, Nielsen ML, Kjeldsen F, Zubarev RA. Proteomics-grade de novo sequencing approach. J. Proteome Res.4(6), 2348–2354 (2005).
  • Frank AM, Savitski MM, Nielsen ML, Zubarev RA, Pevzner PA. De novo peptide sequencing and identification with precision mass spectrometry. J. Proteome Res.6(1), 114–123 (2007).
  • 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(5), 703–714 (2004).
  • Bruce C, Shifman MA, Miller P, Gulcicek EE. Probabilistic enrichment of phosphopeptides by their mass defect. Anal. Chem.78(13), 4374–4382 (2006).
  • Bossio RE, Marshall AG. Baseline resolution of isobaric phosphorylated and sulfated peptides and nucleotides by electrospray ionization FTICR MS: Another step toward mass spectrometry-based proteomics. Anal. Chem.74(7), 1674–1679 (2002).
  • Monigatti F, Hekking B, Steen H. Protein sulfation analysis – a primer. Biochim. Biophys. Acta1764(12), 1904–1913 (2006).
  • Medzihradszky KF, Darula Z, Perlson E et al. O-sulfonation of serine and threonine - mass spectrometric detection and characterization of a new posttranslational modification in diverse proteins throughout the eukaryotes. Mol. Cell. Proteomics3(5), 429–440 (2004).
  • King JB, Gross J, Lovly CM et al. Accurate mass-driven analysis for the characterization of protein phosphorylation. Study of the human Chk2 protein kinase. Anal. Chem.78(7), 2171–2181 (2006).
  • Smyth E, Clegg RA, Holt C. A biological perspective on the structure and function of caseins and casein micelles. Int. J. Dairy Technol.57(2–3), 121–126 (2004).
  • Tsybin YO, Ramstrom M, Witt M, Baykut G, Hakansson P. Peptide and protein characterization by high-rate electron capture dissociation Fourier transform ion cyclotron resonance mass spectrometry. J. Mass Spectrom.39(7), 719–729 (2004).
  • Kjeldsen F, Haselmann KF, Budnik BA, Sorensen ES, Zubarev RA. Complete characterization of posttranslational modification sites in the bovine milk protein PP3 by tandem mass spectrometry with electron capture dissociation as the last stage. Anal. Chem.75(10), 2355–2361 (2003).
  • Abbott KL, Renfrow MB, Chalmers MJ et al. Enhanced binding of RNAP II CTD phosphatase FCP1 to RAP74 following CK2 phosphorylation. Biochemistry44(8), 2732–2745 (2005).
  • Kocher T, Savitski MM, Nielsen ML, Zubarev RA. PhosTShunter: a fast and reliable tool to detect phosphorylated peptides in liquid chromatography Fourier transform tandem mass spectrometry data sets. J. Proteome Res.5(3), 659–668 (2006).
  • Meng FY, Forbes AJ, Miller LM, Kelleher NL. Detection and localization of protein modifications by high resolution tandem mass spectrometry. Mass Spectrom. Rev.24(2), 126–134 (2005).
  • Sze SK, Ge Y, Oh HB, McLafferty FW. Plasma electron capture characterization of large dissociation for the proteins by top down mass spectrometry. Anal. Chem.75(7), 1599–1603 (2003).
  • Thomas CE, Kelleher NL, Mizzen CA. Mass spectrometric characterization of human histone H3: a bird’s eye view. J. Proteome Res.5(2), 240–247 (2006).
  • Garcia BA, Joshi S, Thomas CE et al. Comprehensive phosphoprotein analysis of linker histone H1 from Tetrahymena thermophila. Mol. Cell. Proteomics5(9), 1593–1609 (2006).
  • Coon JJ, Ueberheide B, Syka JEP et al. Protein identification using sequential ion/ion reactions and tandem mass spectrometry. Proc. Natl Acad. Sci. USA102(27), 9463–9468 (2005).
  • Eng JK, McCormack AL, Yates JR III, John R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom.5(11), 976–989 (1994).
  • Perkins DN, Pappin DJC, Creasy DM, Cottrell JS. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis20(18), 3551–3567 (1999).
  • Savitski MM, Kjeldsen F, Nielsen ML, Zubarev RA. Hydrogen rearrangement to and from radical z fragments in electron capture dissociation of peptides. J. Am. Soc. Mass Spectrom.18(1), 113–120 (2007).
  • Savitski MM, Nielsen ML, Zubarev RA. New data base-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(8), 1180–1188 (2005).
  • Liu H, Hakansson K. Electron capture dissociation of tyrosine O-sulfated peptides complexed with divalent metal cations. Anal. Chem.78(21), 7570–7576 (2006).
  • Han X, Jin M, Breuker K, McLafferty FW. Extending top-down mass spectrometry to proteins with masses greater than 200 kilodaltons. Science314(5796), 109–112 (2006).
  • Gunawardena HP, Emory JF, McLuckey SA. Phosphopeptide anion characterization via sequential charge inversion and electron-transfer dissociation. Anal. Chem.78(11), 3788–3793 (2006).
  • Pitteri SJ, McLuckey SA. Recent developments in the ion/ion chemistry of high-mass multiply charged ions. Mass Spectrom. Rev.24(6), 931–958 (2005).

Websites

  • Coon JJ. Electron transfer dissociation: fundamentals and new horizons. Presented at: 4th International Uppsala Conference on Electron Capture and Transfer Dissociation Mass Spectrometry – Fundamental and Applications www.chem.cuhk.edu.hk/uppconIV/main.htm

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.