Enrichment of protein N-termini by charge reversal of internal peptides

Proteomics

Volumn 15, Issue 14, 2015, Pages 2470-2478

  Lai, Zon W ^a   Gomez Auli, Alejandro ^a   Keller, Eva J ^a   Mayer, Bettina ^a   Biniossek, Martin L ^a   Schilling, Oliver ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

Author keywords

N terminomics; Proteases; Proteolysis; TAILS; Technology

Indexed keywords

CATHEPSIN B; CATHEPSIN L; DISINTEGRIN; G PROTEIN COUPLED RECEPTOR; METALLOPROTEINASE; METALLOPROTEINASE DOMAIN CONTAINING PROTEIN 9; METHIONINE; POLYPEPTIDE; PROTEIN; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ANIMAL CELL; ARTICLE; CATION EXCHANGE; COMPARATIVE STUDY; CONTROLLED STUDY; EMBRYO; EMBRYO CELL; FIBROBLAST; ION EXCHANGE CHROMATOGRAPHY; MOLECULAR WEIGHT; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CLEAVAGE; PROTEIN PROCESSING;

EID: 85006380073     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201500023     Document Type: Article

References (28)

1. Kalvik, T. V., Arnesen, T., Protein N-terminal acetyltransferases in cancer. Oncogene 2013, 32, 269–276.
2. Rope, A. F., Wang, K., Evjenth, R., Xing, J. C. et al., Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. Am. J. Hum. Genet.2011, 89, 345-345.
3. Tooley, J. G., Schaner Tooley, C. E., New roles for old modifications: emerging roles of N-terminal post-translational modifications in development and disease. Protein Sci. 2014, 23, 1641–1649.
4. Drew, S. C., Masters, C. L., Barnham, K. J., Alzheimer's A beta peptides with disease-associated N-terminal modifications: influence of isomerisation, truncation and mutation on Cu2+ coordination. Plos One 2010, 5, e15875.
5. Lai, Z. W., Petrera, A., Schilling, O., Protein amino-terminal modifications and proteomic approaches for N-terminal profiling. Curr. Opin. Chem. Biol. 2014, 24C, 71–79.
6. Shen, P. T., Hsu, J. L., Chen, S. H., Dimethyl isotope-coded affinity selection for the analysis of free and blocked N-termini of proteins using LC-MS/MS. Anal. Chem. 2007, 79, 9520–9530.
7. Kleifeld, O., Doucet, A., Keller, U. A. D., Prudova, A. et al., Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products. Nat. Biotechnol 2010, 28, U281–U144.
8. Gevaert, K., Goethals, M., Martens, L., Van Damme, J. et al., Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat. Biotechnol. 2003, 21, 566–569.
9. Venne, A. S., Vogtle, F. N., Meisinger, C., Sickmann, A., Zahedi, R. P., Novel highly sensitive, specific, and straightforward strategy for comprehensive N-terminal proteomics reveals unknown substrates of the mitochondrial peptidase Icp55. J. Proteome Res. 2013, 12, 3823–3830.
10. Guryca, V., Lamerz, J., Ducret, A., Cutler, P., Qualitative improvement and quantitative assessment of N-terminomics. Proteomics 2012, 12, 1207–1216.
11. Tholen, S., Biniossek, M. L., Gansz, M., Ahrens, T. D. et al., Double deficiency of cathepsins B and L results in massive secretome alterations and suggests a degradative cathepsin-MMP axis. Cell. Mol. Life. Sci. 2014, 71, 899–916.
12. Morgenstern, J. P., Land, H., Advanced mammalian gene-transfer—high titer retroviral vectors with multiple-drug selection markers and a complementary helper-free packaging cell-line. Nucleic Acids Res. 1990, 18, 3587–3596.
13. Soneoka, Y., Cannon, P. M., Ramsdale, E. E., Griffiths, J. C. et al., A transient three-plasmid expression system for the production of high titer retroviral vectors. Nucleic Acids Res. 1995, 23, 628–633.
14. Guo, K., Ji, C. J., Li, L., Stable-isotope dimethylation labeling combined with LC-ESI MS for quantification of amine-containing metabolites in biological samples. Anal. Chem. 2007, 79, 8631–8638.
15. Boersema, P. J., Raijmakers, R., Lemeer, S., Mohammed, S., Heck, A. J. R., Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nat. Protocols. 2009, 4, 484–494.
16. Rappsilber, J., Ishihama, Y., Mann, M., Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal. Chem. 2003, 75, 663–670.
17. Shevchenko, A., Tomas, H., Havlis, J., Olsen, J. V., Mann, M., In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat. Protocols 2006, 1, 2856–2860.
18. Pedrioli, P. G., Eng, J. K., Hubley, R., Vogelzang, M. et al., A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol. 2004, 22, 1459–1466.
19. Kessner, D., Chambers, M., Burke, R., Agus, D., Mallick, P., ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 2008, 24, 2534–2536.
20. Craig, R., Beavis, R. C., TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20, 1466–1467.
21. Keller, A., Nesvizhskii, A. I., Kolker, E., Aebersold, R., Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 2002, 74, 5383–5392.
22. Apweiler, R., Martin, M. J., O'Donovan, C., Magrane, M. et al., The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res. 2010, 38, D142–D148.
23. Martens, L., Vandekerckhove, J., Gevaert, K., DBToolkit: processing protein databases for peptide-centric proteomics. Bioinformatics 2005, 21, 3584–3585.
24. Han, D. K., Eng, J., Zhou, H. L., Aebersold, R., Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol. 2001, 19, 946–951.
25. Lange, P. F., Overall, C. M., TopFIND, a knowledgebase linking protein termini with function. Nat. Methods 2011, 8, 703–704.
26. Tholen, S., Biniossek, M. L., Gessler, A. L., Muller, S. et al., Contribution of cathepsin L to secretome composition and cleavage pattern of mouse embryonic fibroblasts. Biol. Chem. 2011, 392, 961–971.
27. Bertaccini, D., Vaca, S., Carapito, C., Arsene-Ploetze, F. et al., An improved stable isotope N-terminal labeling approach with light/heavy TMPP to automate proteogenomics data validation: dN-TOP. J. Proteome Res. 2013, 12, 3063–3070.
28. Van Damme, P., Arnesen, T., Ruttens, B., Gevaert, K., In-gel N-acetylation for the quantification of the degree of protein in vivo N-terminal acetylation. Methods Mol. Biol. 2013, 981, 115–126.