Low-pH solid-phase amino labeling of complex peptide digests with TMTs improves peptide identification rates for multiplexed global phosphopeptide analysis

Journal of Proteome Research

Volumn 14, Issue 6, 2015, Pages 2500-2510

  Böhm, Gitte ^a   Prefot, Petra ^a   Jung, Stephan ^a   Selzer, Stefan ^a   Mitra, Vikram ^b   Britton, David ^b   Kuhn, Karsten ^a   Pike, Ian ^b   Thompson, Andrew H ^b  

^a Proteome Sciences R and D GmbH and Co KG   (Germany)

^b Proteome Sciences plc   (United Kingdom)

Author keywords

chemical labeling; isobaric tags; Mass spectrometry; phosphorylation; proteomics; TMT

Indexed keywords

AMINO ACID; HISTIDINE; PHOSPHOPEPTIDE; THREONINE; TYROSINE; AMINE;

ARTICLE; CONTROLLED STUDY; HUMAN; HUMAN CELL; HUMAN TISSUE; MCF 7 CELL LINE; MULTIPLEXED GLOBAL PHOSPHOPEPTIDE ANALYSIS; PH; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN IMMOBILIZATION; SOLID; STANDARD; TANDEM MASS SPECTROMETRY; CHEMISTRY; TUMOR CELL LINE;

AMINES; CELL LINE, TUMOR; HUMANS; HYDROGEN-ION CONCENTRATION; PHOSPHOPEPTIDES; TANDEM MASS SPECTROMETRY;

EID: 84930583084     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.5b00072     Document Type: Article

References (27)

1. 3+) affinity chromatography Anal. Biochem. 1986, 154, 250-4
2. Posewitz, M. C.; Tempst, P. Immobilized gallium(III) affinity chromatography of phosphopeptides Anal. Chem. 1999, 71, 2883-92
3. Zhou, H.; Ye, M.; Dong, J.; Corradini, E.; Cristobal, A.; Heck, A. J.; Zou, H.; Mohammed, S. Robust phosphoproteome enrichment using monodisperse microsphere-based immobilized titanium (IV) ion affinity chromatography Nat. Protoc. 2013, 8, 461-80
4. Pinkse, M. W.; Uitto, P. M.; Hilhorst, M. J.; Ooms, B.; Heck, A. J. Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns Anal. Chem. 2004, 76, 3935-43
5. Villén, J.; Gygi, S. P. The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry Nat. Protoc. 2008, 3, 1630-8
6. Thompson, A.; Schafer, J.; Kuhn, K.; Kienle, S.; Schwarz, J.; Schmidt, G.; Neumann, T.; Hamon, C. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS Anal. Chem. 2003, 75, 1895-904
7. Werner, T.; Becher, I.; Sweetman, G.; Doce, C.; Savitski, M. M.; Bantscheff, M. High-resolution enabled TMT 8-plexing Anal. Chem. 2012, 84, 7188-94
8. McAlister, G. C.; Huttlin, E. L.; Haas, W.; Ting, L.; Jedrychowski, M. P.; Rogers, J. C.; Kuhn, K.; Pike, I.; Grothe, R. A.; Blethrow, J. D.; Gygi, S. P. Increasing the multiplexing capacity of TMTs using reporter ion isotopologues with isobaric masses Anal. Chem. 2012, 84, 7469-78
9. Erickson, B. K.; Jedrychowski, M. P.; McAlister, G. C.; Everley, R. A.; Kunz, R.; Gygi, S. P. Evaluating multiplexed quantitative phosphopeptide analysis on a hybrid quadrupole mass filter/linear ion trap/orbitrap mass spectrometer Anal. Chem. 2015, 87, 1241-9
10. Britton, D.; Zen, Y.; Quaglia, A.; Selzer, S.; Mitra, V.; Lobetaner, C.; Jung, S.; Bohm, G.; Schmid, P.; Prefot, P.; Hoehle, C.; Koncarevic, S.; Gee, J.; Nicholson, R.; Ward, M.; Castellano, L.; Stebbing, J.; Zucht, H. D.; Sarker, D.; Heaton, N.; Pike, I. Quantification of pancreatic cancer proteome and phosphorylome: indicates molecular events likely contributing to cancer and activity of drug targets PLoS One 2014, 9, e90948
11. Cindric, M.; Cepo, T.; Skrlin, A.; Vuletic, M.; Bindila, L. Accelerated on-column lysine derivatization and cysteine methylation by imidazole reaction in a deuterated environment for enhanced product ion analysis Rapid Commun. Mass Spectrom. 2006, 20, 694-702
12. Conrotto, P.; Hellman, U. Sulfonation chemistry as a powerful tool for MALDI TOF/TOF de novo sequencing and post-translational modification analysis J. Biomol. Tech. 2005, 16, 441-52
13. Boersema, P. J.; Raijmakers, R.; Lemeer, S.; Mohammed, S.; Heck, A. J. Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics Nat. Protoc. 2009, 4, 484-94
14. Nika, H.; Lee, J.; Willis, I. M.; Angeletti, R. H.; Hawke, D. H. Phosphopeptide characterization by mass spectrometry using reversed-phase supports for solid-phase beta-elimination/Michael addition J. Biomol. Tech. 2012, 23, 51-68
15. Perkins, D. N.; Pappin, D. J.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 1999, 20, 3551-67
16. Yates, J. R.; Eng, J. K.; McCormack, A. L.; Schieltz, D. Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database Anal. Chem. 1995, 67, 1426-36
17. Kall, L.; Canterbury, J. D.; Weston, J.; Noble, W. S.; MacCoss, M. J. Semi-supervised learning for peptide identification from shotgun proteomics datasets Nat. Methods 2007, 4, 923-5
18. Taus, T.; Kocher, T.; Pichler, P.; Paschke, C.; Schmidt, A.; Henrich, C.; Mechtler, K. Universal and confident phosphorylation site localization using phosphoRS J. Proteome Res. 2011, 10, 5354-62
19. Elias, J. E.; Gygi, S. P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry Nat. Methods 2007, 4, 207-14
20. Thingholm, T. E.; Palmisano, G.; Kjeldsen, F.; Larsen, M. R. Undesirable charge-enhancement of isobaric tagged phosphopeptides leads to reduced identification efficiency J. Proteome Res. 2010, 9, 4045-52
21. Pichler, P.; Kocher, T.; Holzmann, J.; Mazanek, M.; Taus, T.; Ammerer, G.; Mechtler, K. Peptide labeling with isobaric tags yields higher identification rates using iTRAQ 4-plex compared to TMT 6-plex and iTRAQ 8-plex on LTQ Orbitrap Anal. Chem. 2010, 82, 6549-58
22. Altelaar, A. F.; Frese, C. K.; Preisinger, C.; Hennrich, M. L.; Schram, A. W.; Timmers, H. T.; Heck, A. J.; Mohammed, S. Benchmarking stable isotope labeling based quantitative proteomics J. Proteomics 2013, 88, 14-26
23. Woods, A. G.; Sokolowska, I.; Darie, C. C. Identification of consistent alkylation of cysteine-less peptides in a proteomics experiment Biochem. Biophys. Res. Commun. 2012, 419, 305-8
24. Kollipara, L.; Zahedi, R. P. Protein carbamylation: in vivo modification or in vitro artefact? Proteomics 2013, 13, 941-4
25. Ting, L.; Rad, R.; Gygi, S. P.; Haas, W. MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics Nat. Methods 2011, 8, 937-40
26. Kulak, N. A.; Pichler, G.; Paron, I.; Nagaraj, N.; Mann, M. Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells Nat. Methods 2014, 11, 319-24
27. Wisniewski, J. R.; Zougman, A.; Mann, M. Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome J. Proteome Res. 2009, 8, 5674-8