Strategies in protein sequencing and characterization: Multi-enzyme digestion coupled with alternate CID/ETD tandem mass spectrometry

Analytica Chimica Acta

Volumn 854, Issue , 2015, Pages 106-117

  Nardiello, Donatella ^a   Palermo, Carmen ^a   Natale, Anna ^a   Quinto, Maurizio ^a   Centonze, Diego ^a  

^a UNIVERSITY OF FOGGIA   (Italy)

Author keywords

Collision induced dissociation; Electron transfer dissociation; Enzymatic digestion; Post translational modifications; Sequence variants; Species specific residues

Indexed keywords

ELECTRON TRANSITIONS; ELECTROPHORESIS; ENZYMES; IONS; MASS SPECTROMETRY; PEPTIDES; PROTEOMICS; SEARCH ENGINES;

COLLISION INDUCED DISSOCIATION; ELECTRON TRANSFER DISSOCIATION; ENZYMATIC DIGESTIONS; POST-TRANSLATIONAL MODIFICATIONS; SEQUENCE VARIANTS; SPECIES SPECIFICS;

DISSOCIATION;

ALPHA CASEIN; ALPHA LACTOGLOBULIN; BETA CASEIN; BETA LACTOGLOBULIN; BOVINE SERUM ALBUMIN; CHYMOTRYPSIN; KAPPA CASEIN; LACTOGLOBULIN; MILK PROTEIN; PROTEASE LYS C; PROTEINASE; TRYPSIN; UNCLASSIFIED DRUG; ENZYME; PROTEIN;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; COLLISIONALLY ACTIVATED DISSOCIATION; CONTROLLED STUDY; ELECTRON TRANSFER DISSOCIATION; ENZYMATIC DEGRADATION; EXPERIMENTAL DESIGN; EXPERIMENTAL STUDY; FALSE POSITIVE RESULT; FEASIBILITY STUDY; FRAGMENTATION REACTION; GOAT MILK; INCUBATION TIME; INTERMETHOD COMPARISON; LIQUID CHROMATOGRAPHY; MEASUREMENT ACCURACY; MOLECULAR WEIGHT; MULTI ENZYME DIGESTION; NANOLIQUID CHROMATOGRAPHY; NONHUMAN; PROTEIN ANALYSIS; PROTEIN CLEAVAGE; PROTEIN LOCALIZATION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEOMICS; SEPARATION TECHNIQUE; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; TANDEM MASS SPECTROMETRY; TWO DIMENSIONAL ELECTROPHORESIS; VALIDATION PROCESS; ANIMAL; CHEMISTRY; PROCEDURES;

ANIMALIA; CAPRA HIRCUS;

ANIMALS; CHROMATOGRAPHY, LIQUID; ENZYMES; PROTEINS; TANDEM MASS SPECTROMETRY;

EID: 84919371899     PISSN: 00032670     EISSN: 18734324     Source Type: Journal    
DOI: 10.1016/j.aca.2014.10.053     Document Type: Article

References (61)

1. Boersema P.J., Mohammed S., Heck A.J.R. Phosphopeptide fragmentation and analysis by mass spectrometry. J. Mass Spectrom. 2009, 44:861-878.
2. Mikesh L.M., Ueberheide B., Chi A., Coon J.J., Syka J.E.P., Shabanowitz J., Hunt D.F. The utility of ETD mass spectrometry in proteomic analysis. Biochim. Biophys. Acta 2006, 1764:1811-1822.
3. Villèn J., Beausoleil S.A., Gygi S.P. Evaluation of the utility of neutral-loss-dependent MS3 strategies in large-scale phosphorylation analysis. Proteomics 2008, 8:4444-4452.
4. Rožman M., Gaskell S.J. Charge state dependent top-down characterisation using electron transfer dissociation. Rapid Commun. Mass Spectrom. 2012, 26:282-286.
5. Palumbo A.M., Smith S.A., Kalcic C.L., Dantus M., Stemmer P.M., Reid G.E. Tandem mass spectrometry strategies for phosphoproteome analysis. Mass Spectrom. Rev. 2011, 30:600-625.
6. Kim M.S., Zhong J., Kandasamy K., Delanghe B., Pandey A. Systematic evaluation of alternating CID and ETD fragmentation for phosphorylated peptides. Proteomics 2011, 11:2568-2572.
7. Chait B.T. Extending top-down mass spectrometry to proteins with masses greater than 200kDa. Science 2006, 314:65-66.
8. Hu L., Ye M., Jiang X., Feng S., Zou H. Advances in hyphenated analytical techniques for shotgun proteome and peptidome analysis. Anal. Chim. Acta 2007, 598:193-204.
9. Mann M., Jensen O.N. Proteomic analysis of post-translational modifications. Nat. Biotechnol. 2003, 21:255-261.
10. Gnad F., de Godoy L., Neuhauser N., Ren S., Olsen J., Mann M. High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast. Proteomics 2009, 9:4642-4652.
11. McGivern J., Swaney D., Coon J., Sheets M. Toward defining the phosphoproteome of Xenopus laevis embryos. Dev. Dynam. 2009, 238:1433-1443.
12. Hoffman M.D., Sniatynski M.J., Kast J. Current approaches for global post-translational modification discovery and mass spectrometric analysis. J. Anal. Chem. 2008, 627:50-61.
13. Creese A., Cooper H.J. The effect of phosphorylation on the electron capture dissociation of peptide ions. J. Am. Soc. Mass Spectrom. 2008, 19:1263-1274.
14. MacCoss M.J., McDonald W.H., Saraf A., Sadygov R., Clark J.M., Tasto J.J., Gould K.L., Wolters D., Washburn M., Weiss A., Clark J.I., Yates J.R. Shotgun identification of protein modifications from protein complexes and lens tissue. Proc. Natl. Acad. Sci. U. S. A. 2002, 99:7900-7905.
15. Ishihama Y., Wei F., Aoshima K., Sato T., Kuromitsu J., Oda Y. Enhancement of the efficiency of phosphoproteomic identification by removing phosphates after phosphopeptide enrichment. J. Proteome Res. 2007, 6:1139-1144.
16. Marcantonio M., Trost M., Courcelles M., Desjardins M., Thibault P. Combined enzymatic and data mining approaches for comprehensive phosphoproteome analyses. Mol. Cell. Proteomics 2008, 7:645-660.
17. Chait B.T., Wang R., Beavis R.C., Kent S.B. Protein ladder sequencing. Science 1993, 262:89-92.
18. Thingholm T.E., Jensen O.N., Larsen M.R. Analytical strategies for phosphoproteomics. Proteomics 2009, 9:1451-1468.
19. Huzarska M., Ugalde I., Kaplan D.A., Hartmer R., Easterling M.L., Polfer N.C. Negative electron transfer dissociation of deprotonated phosphopeptide anions: choice of radical cation reagent and competition between electron and proton transfer. Anal. Chem. 2010, 82:2873-2878.
20. Coon J.J., Syka J.E.P., Shabanowitz J., Hunt D.F. Tandem mass spectrometry for peptide and protein sequence analysis. BioTechniques 2005, 38:519-523.
21. -. Anal. Chem. 2005, 77:1831-1839.
22. Wiesner J., Premsler T., Sickmann A. Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications. Proteomics 2008, 8:4466-4483.
23. Kjeldsen F., Giessing A.M.B., Ingrell C.R., Jensen O.N. Peptide sequencing and characterization of post-translational modifications by enhanced ion-charging and liquid chromatography electron-transfer dissociation tandem mass spectrometry. Anal. Chem. 2007, 79:9243-9252.
24. Molina H., Matthiesen R., Kandasamy K., Pandey A. Comprehensive comparison of collision induced dissociation and electron transfer dissociation. Anal. Chem. 2008, 80:4825-4835.
25. Sweet S.M.M., Bailey C.M., Cunningham D.L., Heath J.K., Cooper H.J. Large scale localization of protein phosphorylation by use of electron capture dissociation mass spectrometry. Mol. Cell. Proteomics 2009, 8:904-912.
26. Syka J.E.P., Coon J.J., Schroeder M.J., Shabanowitz J., Hunt D.F. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 2004, 101:9528-9533.
27. Kim M.S., Pandey A. Electron transfer dissociation mass spectrometry in proteomics. Proteomics 2012, 12:530-542.
28. Campbell J.L., Hager J.W., Yves Le Blanc J.C. On performing simultaneous electron transfer dissociation and collision-induced dissociation on multiply protonated peptides in a linear ion trap. J. Am. Soc. Mass Spectrom. 2009, 20:1672-1683.
29. Good M.D., Wirtala M., McAlister G.C., Coon J.J. Performance characteristics of electron transfer dissociation mass spectrometry. Mol. Cell. Proteomics 2007, 6:1942-1951.
30. Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F. Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 2007, 104:2193-2198.
31. Kelleher R.L., Zubarev R.A., Bush K., Furie B.C., McLafferty F.W., Walsh C.T. Localization of labile posttranslational modifications by electron capture dissociation: the case of γ-carboxyglutamic acid. Anal. Chem. 1999, 71:4250-4253.
32. Molina H., Horn D.M., Tang N., Mathivanan S., Pandey A. Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 2007, 104:2199-2204.
33. Swaney D.L., McAlister G.C., Coon J.J. Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nat. Met. 2008, 5:959-964.
34. Meyer B., Papasotiriou D.G., Karas M. Decision tree-driven tandem mass spectrometry for shotgun proteomics. Amino Acids 2011, 4:291-310.
35. Huang Y.Y., Tseng G.C., Yuan S.S., Pasa-Tolic L., Lipton M.S., Smith R.D., Wysocki V.H. A data-mining scheme for identifying peptide structural motifs responsible for different MS/MS fragmentation intensity patterns. J. Proteome Res. 2008, 7:70-79.
36. Martin D.B., Eng J.K., Nesvizhskii A.I., Gemmill A., Aebersold R. Investigation of neutral loss during collision-induced dissociation of peptide ions. Anal. Chem. 2005, 77:4870-4882.
37. Taouatas N., Drugan M.M., Heck A.J., Mohammed S. Straightforward ladder sequencing of peptides using a Lys-N metalloendopeptidase. Nat. Met. 2008, 5:405-407.
38. Chalkley R.J., Medzihradszky K.F., Lynn A.J., Baker P.R., Burlingame A.L. Statistical analysis of peptide electron transfer dissociation fragmentation mass spectrometry. Anal. Chem. 2010, 82:579-589.
39. Kalli A., Håkansson K. Comparison of the electron capture dissociation fragmentation behavior of doubly and triply protonated peptides from trypsin Glu-C, and chymotrypsin digestion. J. Proteome Res. 2008, 7:2834-2844.
40. Zhang Y., Fonslow B.R., Shan B., Baek M.C., Yates J.R. Protein analysis by shot-gun/bottom-up proteomics. Chem. Rev. 2013, 113:2343-2394.
41. Switzar L., Giera M., Niessen W.M.A. Protein digestion: an overview of the avalilable techniques and recent developments. J. Proteome Res. 2013, 12:1067-1077.
42. Speers A.E., Wu C.C. Proteomics of integral membrane proteins-theory and application. Chem Rev. 2007, 107:3687-3714.
43. Golizeh M., Sleno L. Optimized proteomic analysis of rat liver microsomes using dual enzyme digestion with 2D-LC-MS/MS. J. Proteomics 2013, 82:166-178.
44. Vermachova M., Purkrtova Z., Santrucek J., Jolivet P., Chardot T., Kodicek M. Combining chymotrypsin/trypsin digestion to identify hydrophobic proteins from oil bodies. Methods Mol. Biol. 2014, 1072:185-198.
45. Chiva C., Ortega M., Sabidó E. Influence of the digestion technique, protease, and missed cleavage peptides in protein quantitation. J. Proteome Res. 2014, 13:3979-3986.
46. Swaney D.L., Wenger C.D., Coon J.J. Value of using multiple proteases for large-scale mass spectrometry-based proteomics. J. Proteome Res. 2010, 9:1323-1329.
47. Fischer F., Wolters D., Rögner M., Poetsch A. High coverage of integral membrane proteins through transmembrane peptide detection. Mol. Cell. Proteomics 2006, 5:444-453.
48. Fischer F., Poetsch A. Protein cleavage strategies for an improved analysis of the membrane proteome. Proteome Sci. 2006, 4. art. no. 2.
49. Chmelik J., Zidkova J., Rehulka P., Petry-Podgorska I., Bobalova J. Influence of different proteomic protocols on degree of high-coverage identification of nonspecific lipid transfer protein 1 modified during malting. Electrophoresis 2009, 30:560-567.
50. Li W., Song C., Bailey D.J., Tseng G.C., Coon J.J., Wysocki V.H. Statistical analysis of electron transfer dissociation pairwise fragmentation patterns. Anal. Chem. 2011, 83:9540-9545.
51. Cook S.L., Zimmermann C.M., Singer D., Fedorova M., Hoffmann R., Jackson G.P. Comparison of CID, ETD and metastable atom-activated dissociation (MAD) of doubly and triply charged phosphorylated tau peptides. J. Mass Spectrom. 2012, 47:786-794.
52. Ni W., Lin M., Salinas P., Savickas P., Wu B.L., Karger S.-L. Complete mapping of a cystine knot and nested disulfides of recombinant human arylsulfatase a by multi-enzyme digestion and LC-MS analysis using CID and ETD. J. Am. Soc. Mass Spectrom. 2013, 24:125-133.
53. Bonilla L.E., Means G.D., Lee K.A., Patterson S.D. The evolution of tools for protein phosphorylation site analysis: from discovery to clinical application. BioTechniques 2008, 44:671-679.
54. Dykstra A.B., Rodriguez M., Raman B., Cook K.D., Hettich R.L. Characterizing the range of extracellular protein post-translational modifications in a cellulose-degrading bacteria using a multiple proteolyic digestion/peptide fragmentation approach. Anal. Chem. 2013, 85:3144-3151.
55. Westermeier R., Görg A. Protein Purification 2011, John Wiley & Sons, Hoboken, New Jersey USA. J.C. Janson (Ed.).
56. Alves P., Arnold R.J., Clemmer D.E., Li Y., Reilly J.P., Sheng Q., Tang H., Xun Z., Zeng R., Radivojac P. Fast and accurate identification of semi-tryptic peptides in shotgun proteomics. Bioinformatics 2008, 24:102-109.
57. Losito I., Carbonara T., De Bari M.D., Gobbetti M., Palmisano F., Rizzello C.G., Zambonin P.G. Identification of peptides in antimicrobial fractions of cheese extracts by electrospray ionization ion trap mass spectrometry coupled to a two-dimensional liquid chromatographic separation. Rapid Commun. Mass Spectrom. 2006, 20:447-455.
58. Kim M.S., Zhong J., Kandasamy K., Delanghe B., Pandey A. Systematic evaluation of alternating CID and ETD fragmentation for phosphorylated peptides. Proteomics 2011, 11:2568-2572.
59. Savitski M.M., Lemeer S., Boesche M., Lang M., Mathieson T., Bantscheff M., Kuster B. Confident phosphorylation site localization using the Mascot delta score. Mol. Cell Proteomics 2011, 10. M110.003830.
60. Dephoure N., Gould K.L., Gygi S.P., Kellogg D.R. Mapping and analysis of phosphorylation sites: a quick guide for cell biologists. Mol. Biol. Cell. 2013, 24:535-542.
61. Wiese H., Kuhlmann K., Wiese S., Stoepel N.S., Pawlas M., Meyer H.E., Stephan C., Eisenacher M., Drepper F., Warscheid B. Comparison of alternative MS/MS and bioinformatics approaches for confident phosphorylation site localization. J. Proteome Res. 2014, 13:1128-1137.