Large Scale Localization of Protein Phosphorylation by Use of Electron Capture Dissociation Mass Spectrometry

We used on-line electron capture dissociation (ECD) for the large scale identification and localization of sites of phosphorylation. Each FT-ICR ECD event was paired with a linear ion trap collision-induced dissociation (CID) event, allowing a direct comparison of the relative merits of ECD and CID for phosphopeptide identification and site localization. Linear ion trap CID was shown to be most efficient for phosphopeptide identification, whereas FT-ICR ECD was superior for localization of sites of phosphorylation. The combination of confident CID and ECD identification and confident CID and ECD localization is particularly valuable in cases where a phosphopeptide is identified just once within a phosphoproteomics experiment.

[1]  S. Bryant,et al.  Open mass spectrometry search algorithm. , 2004, Journal of proteome research.

[2]  H. Cooper,et al.  Targeted online liquid chromatography electron capture dissociation mass spectrometry for the localization of sites of in vivo phosphorylation in human Sprouty2. , 2008, Analytical Chemistry.

[3]  J. Olsen,et al.  Electron capture dissociation of singly and multiply phosphorylated peptides. , 2000, Rapid communications in mass spectrometry : RCM.

[4]  Lewis Y. Geer,et al.  Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry , 2007, Proceedings of the National Academy of Sciences.

[5]  Brian E. Ruttenberg,et al.  PhosphoScore: an open-source phosphorylation site assignment tool for MSn data. , 2008, Journal of proteome research.

[6]  F W McLafferty,et al.  Localization of labile posttranslational modifications by electron capture dissociation: the case of gamma-carboxyglutamic acid. , 1999, Analytical chemistry.

[7]  M. Larsen,et al.  SIMAC (Sequential Elution from IMAC), a Phosphoproteomics Strategy for the Rapid Separation of Monophosphorylated from Multiply Phosphorylated Peptides*S , 2008, Molecular & Cellular Proteomics.

[8]  Ronald J Moore,et al.  Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags. , 2008, Analytical chemistry.

[9]  Stefani N. Thomas,et al.  PhosphoScan: a probability-based method for phosphorylation site prediction using MS2/MS3 pair information. , 2008, Journal of proteome research.

[10]  H. Cooper,et al.  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 , 2007, Journal of the American Society for Mass Spectrometry.

[11]  H. Cooper,et al.  The role of electron capture dissociation in biomolecular analysis. , 2005, Mass spectrometry reviews.

[12]  F. McLafferty,et al.  Electron Capture Dissociation of Multiply Charged Protein Cations. A Nonergodic Process , 1998 .

[13]  K. Masuda,et al.  Fast multiple electron capture dissociation in a linear radio frequency quadrupole ion trap. , 2007, Analytical chemistry.

[14]  Amanda M Palumbo,et al.  Evaluation of gas-phase rearrangement and competing fragmentation reactions on protein phosphorylation site assignment using collision induced dissociation-MS/MS and MS3. , 2008, Analytical chemistry.

[15]  J. Shabanowitz,et al.  Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[16]  L. Ding,et al.  Electron capture dissociation in a digital ion trap mass spectrometer. , 2006, Analytical chemistry.

[17]  M. Savitski,et al.  Electron capture/transfer versus collisionally activated/induced dissociations: Solo or duet? , 2008, Journal of the American Society for Mass Spectrometry.

[18]  G. McAlister,et al.  Performance Characteristics of Electron Transfer Dissociation Mass Spectrometry*S , 2007, Molecular & Cellular Proteomics.

[19]  J. Shabanowitz,et al.  Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae , 2002, Nature Biotechnology.

[20]  Steven P Gygi,et al.  A probability-based approach for high-throughput protein phosphorylation analysis and site localization , 2006, Nature Biotechnology.

[21]  M. Savitski,et al.  Proteomics-grade de novo sequencing approach. , 2005, Journal of proteome research.

[22]  M. Savitski,et al.  Immunoaffinity enrichments followed by mass spectrometric detection for studying global protein tyrosine phosphorylation. , 2008, Journal of proteome research.

[23]  Mikhail M Savitski,et al.  Improving Protein Identification Using Complementary Fragmentation Techniques in Fourier Transform Mass Spectrometry* , 2005, Molecular & Cellular Proteomics.

[24]  N. Blom,et al.  Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. , 1999, Journal of molecular biology.

[25]  J. Rush,et al.  Immunoaffinity profiling of tyrosine phosphorylation in cancer cells , 2005, Nature Biotechnology.

[26]  M. Larsen,et al.  Highly selective enrichment of phosphorylated peptides using titanium dioxide , 2006, Nature Protocols.

[27]  A. Pandey,et al.  Comprehensive Comparison of Collision Induced Dissociation and Electron Transfer Dissociation , 2008, Analytical chemistry.

[28]  M. Savitski,et al.  On studying protein phosphorylation patterns using bottom-up LC-MS/MS: the case of human alpha-casein. , 2007, The Analyst.

[29]  M. Mann,et al.  Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks , 2006, Cell.

[30]  C. Nilsson,et al.  Identification of single and double sites of phosphorylation by ECD FT-ICR/MS in peptides related to the phosphorylation site domain of the myristoylated alanine-rich c kinase protein , 2007, Journal of the American Society for Mass Spectrometry.

[31]  Steve M M Sweet,et al.  Strategy for the identification of sites of phosphorylation in proteins: neutral loss triggered electron capture dissociation. , 2006, Analytical chemistry.

[32]  R. Zubarev,et al.  Localization of O-glycosylation sites in peptides by electron capture dissociation in a Fourier transform mass spectrometer. , 1999, Analytical chemistry.

[33]  Martin Zeller,et al.  SLoMo: automated site localization of modifications from ETD/ECD mass spectra. , 2009, Journal of proteome research.

[34]  Suresh Mathivanan,et al.  Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry , 2007, Proceedings of the National Academy of Sciences.

[35]  Mikhail M Savitski,et al.  Side-chain losses in electron capture dissociation to improve peptide identification. , 2007, Analytical chemistry.

[36]  D. N. Perkins,et al.  Probability‐based protein identification by searching sequence databases using mass spectrometry data , 1999, Electrophoresis.

[37]  H. Cooper,et al.  Electron capture dissociation in the analysis of protein phosphorylation , 2007, Expert review of proteomics.

[38]  H. Cooper,et al.  The Effect of Phosphorylation on the Electron Capture Dissociation of Peptide Ions , 2008, Journal of the American Society for Mass Spectrometry.

[39]  J. Heath,et al.  The Deleted in Brachydactyly B Domain of ROR2 Is Required for Receptor Activation by Recruitment of Src , 2008, PloS one.

[40]  Roman A. Zubarev,et al.  Hydrogen rearrangement to and from radical z fragments in electron capture dissociation of peptides , 2007, Journal of the American Society for Mass Spectrometry.

[41]  H. Cooper,et al.  Data-dependent electron capture dissociation FT-ICR mass spectrometry for proteomic analyses. , 2005, Journal of proteome research.