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References

  • 1 Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, Lander ES. Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci U S A 2007;104:19428-19433.
  • 2 Consortium TU. UniProt: a hub for protein information. Nucleic Acids Res 2015;43:D204-D212.
  • 3 Ayoubi TA, Ven WJVD. Regulation of gene expression by alternative promoters. FASEB J 1996;10:453-460.
  • 4 Jensen ON. Modification-specific proteomics: characterization of posttranslational modifications by mass spectrometry. Curr Opin Chem Biol 2004;8:33-41.
  • 5 Walsh C. Post-translational Modification of Proteins: Expanding Nature’s Inventory. Roberts and Company Publishers; 2006.
  • 6 Johnson LN. The regulation of protein phosphorylation. Biochem Soc Trans 2009;37:627-641.
  • 7 Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S. The protein kinase complement of the human genome. Science 2002;298:1912-1934.
  • 8 Dever TE, Gutierrez E, Shin B-S. The hypusine-containing translation factor eIF5A. Crit Rev Biochem Mol Biol 2014;49:413-425.
  • 9 Komander D, Rape M. The ubiquitin code. Annu Rev Biochem 2012;81:203-229.
  • 10 Bannister AJ, Kouzarides T. Regulation of chromatin by histone modifications. Cell Res 2011;21:381-395.
  • 11 Hunter T. The age of crosstalk: phosphorylation, ubiquitination, and beyond. Mol Cell 2007;28:730-738.
  • 12 Ordureau A, Sarraf SA, Duda DM, Heo J-M, Jedrychowski MP, Sviderskiy VO, Olszewski JL, Koerber JT, Xie T, Beausoleil SA, Wells JA, Gygi SP, Schulman BA, Harper JW. Quantitative proteomics reveal a feedforward mechanism for mitochondrial PARKIN translocation and ubiquitin chain synthesis. Mol Cell 2014;56:360-375.
  • 13 Villen J, Gygi SP. The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry. Nat Protoc 2008;3:1630-1638.
  • 14 Stenflo J, Fernlund P, Egan W, Roepstorff P. Vitamin K dependent modifications of glutamic acid residues in prothrombin. Proc Natl Acad Sci U S A 1974;71:2730-2733.
  • 15 Nesvizhskii AI. Protein identification by tandem mass spectrometry and sequence database searching. In: Mass Spectrometry Data Analysis in Proteomics. New Jersey: Humana Press; 2006. p 87-120.
  • 16 Anania VG, Pham VC, Huang X, Masselot A, Lill JR, Kirkpatrick DS. Peptide level immunoaffinity enrichment enhances ubiquitination site identification on individual proteins. Mol Cell Proteomics 2014;13:145-156.
  • 17 Anderson NL, Anderson NG, Haines LR, Hardie DB, Olafson RW, Pearson TW. Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA).

JProteome Res 2004;3:235-244.

  • 18 Kuhn E, Addona T, Keshishian H, Burgess M, Mani DR, Lee RT, Sabatine MS, Gerszten RE, Carr SA. Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry. Clin Chem 2009;55:1108-1117.
  • 19 Gruhler A, Olsen JV, Mohammed S, Mortensen P, Fargeman NJ, Mann M, Jensen ON. Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol Cell Proteomics 2005;4:310-327.
  • 20 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 Proteomics 2005;4:873-886.
  • 21 Wolschin F, Wienkoop S, Weckwerth W. Enrichment of phosphorylated proteins and peptides from complex mixtures using metal oxide/hydroxide affinity chromatography (MOAC). Proteomics 2005;5:4389-4397.
  • 22 Fila J, Honys D. Enrichment techniques employed in phosphoproteomics. Amino Acids 2012;43:1025-1047.
  • 23 Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 2003;422:198-207.
  • 24 McLafferty FW, Horn DM, Breuker K, Ge Y, Lewis MA, Cerda B, Zubarev RA, Carpenter BK. Electron capture dissociation of gaseous multiply charged ions by Fourier-transform ion cyclotron resonance. J Am Soc Mass Spectrom 2001;12:245-249.
  • 25 Syka JEP, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci U S A 2004;101:9528-9533.
  • 26 Wells JM, McLuckey SA. Collision-induced dissociation (CID) of peptides and proteins. Methods Enzymol 2005;402:148-185.
  • 27 Han J, Borchers CH. Top-down analysis of recombinant histone H3 and its methylated analogs by ESI/FT-ICR mass spectrometry. Proteomics 2010;10:3621-3630.
  • 28 Moradian A, Kalli A, Sweredoski MJ, Hess S. The top-down, middle-down, and bottom-up mass spectrometry approaches for characterization of histone variants and their post-translational modifications. Proteomics 2014;14:489-497.
  • 29 Sidoli S, Lin S, Karch KR, Garcia BA. Bottom-up and middle-down proteomics have comparable accuracies in defining histone post-translational modification relative abundance and stoichiometry. Anal Chem 2015;87:3129-3133.
  • 30 Eng JK, McCormack AL, Yates JR. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database.

J Am Soc Mass Spectrom 1994;5:976-989.

  • 31 Perkins DN, Pappin DJC, Creasy DM, Cottrell JS. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999;20:3551-3567.
  • 32 Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M. Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res 2011; 10:1794-1805.
  • 33 Egertson JD, Kuehn A, Merrihew GE, Bateman NW, MacLean BX, Ting YS, Canterbury JD, Marsh DM, Kellmann M, Zabrouskov V, Wu CC, MacCoss MJ. Multiplexed MS/MS for improved data independent acquisition. Nat Methods 2013;10:744-746.
  • 34 Distler U, Kuharev J, Navarro P, Levin Y, Schild H, Tenzer S. Drift time- specific collision energies enable deep-coverage data-independent acquisition proteomics. Nat Methods 2014;11:167-170.
  • 35 Rost HL, Rosenberger G, Navarro P, Gillet L, Miladinovic SM, Schubert OT, Wolski W, Collins BC, Malmstrom J, Malmstrom L, Aebersold R. OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nat Biotechnol 2014;32:219-223.
  • 36 Parker BL, Yang G, Humphrey SJ, Chaudhuri R, Ma X, Peterman S, James DE. Targeted phosphoproteomics of insulin signaling using data-independent acquisition mass spectrometry. Sci Signal 2015;8:rs6-rs6.
  • 37 Sidoli S, Lin S, Xiong L, Bhanu NV, Karch KR, Johansen E, Hunter C, Mollah S, Garcia BA. Sequential window acquisition of all theoretical mass spectra (SWATH) analysis for characterization and quantification of histone posttranslational modifications. Mol Cell Proteomics 2015;14:2420-2428.
  • 38 Picotti P, Aebersold R. Selected reaction monitoring-based proteomics: workflows, potential pitfalls and future direction. Nat Methods 2012;9(6):555-566.
  • 39 Annan RS, Carr SA. The essential role of mass spectrometry in characterizing protein structure: mapping post-translational modifications. JProtein Chem 1997;16:391-402.
  • 40 Casado-Vela J, Ruiz EJ, Nebreda AR, Casal JI. A combination of neutral loss and targeted product ion scanning with two enzymatic digestions facilitates the comprehensive mapping of phosphorylation sites. Proteomics 2007;7:2522-2529.
  • 41 Mead JA, Bianco L, Ottone V, Barton C, Kay RG, Lilley KS, Bond NJ, Bessant C. MRMaid, the web-based tool for designing multiple reaction monitoring (MRM) transitions. Mol Cell Proteomics 2009;8:696-705.
  • 42 MacLean B, Tomazela DM, Shulman N, Chambers M, Finney GL, Frewen B, Kern R, Tabb DL, Liebler DC, MacCoss MJ. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 2010;26:966-968.
  • 43 Unwin RD, Griffiths JR, Leverentz MK, Grallert A, Hagan IM, Whetton AD. Multiple reaction monitoring to identify sites of protein phosphorylation with high sensitivity. Mol Cell Proteomics 2005;4:1134-1144.
  • 44 Evans CA, Griffiths JR, Unwin RD, Whetton AD, Corfe BM. Application of the MIDAS approach for analysis of lysine acetylation sites. In: Hake SB, Janzen CJ, editors. Protein Acetylation. Totowa, NJ: Humana Press; 2013. p 25-36.
  • 45 Unwin RD, Griffiths JR, Whetton AD. A sensitive mass spectrometric method for hypothesis-driven detection of peptide post-translational modifications: multiple reaction monitoring-initiated detection and sequencing (MIDAS). Nat Protoc 2009;4:870-877.
  • 46 Mollah S, Wertz IE, Phung Q, Arnott D, Dixit VM, Lill JR. Targeted mass spectrometric strategy for global mapping of ubiquitination on proteins.

Rapid Commun Mass Spectrom RCM 2007;21:3357-3364.

  • 47 Choudhary C, Mann M. Decoding signalling networks by mass spectrometry- based proteomics. Nat Rev Mol Cell Biol 2010;11:427-439.
  • 48 Patterson SD. Data analysis-the Achilles heel of proteomics. Nat Biotechnol 2003;21:221-222.
  • 49 Carr S, Aebersold R, Baldwin M, Burlingame A, Clauser K, Nesvizhskii A. The need for guidelines in publication of peptide and protein identification data working group on publication guidelines for peptide and protein identification data. Mol Cell Proteomics 2004;3:531-533.
  • 50 Cox J, Mann M. Quantitative, high-resolution proteomics for data-driven systems biology. Annu Rev Biochem 2011;80:273-299.
  • 51 Nesvizhskii AI, Vitek O, Aebersold R. Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods 2007;4:787-797.
  • 52 Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 2008;26:1367-1372.
  • 53 Houel S, Abernathy R, Renganathan K, Meyer-Arendt K, Ahn NG, Old WM. Quantifying the impact of chimera MS/MS spectra on peptide identification in large-scale proteomics studies. JProteome Res 2010;9:4152-4160.
  • 54 Clauser KR, Baker P, Burlingame AL. Protein prospector role of accurate mass measurement (±10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal Chem 1999;71:2871-2882.
  • 55 Bern M, Kil YJ, Becker C. Byonic: advanced peptide and protein identification software. Curr Protoc Bioinforma 2012;Chapter 13:Unit13.20.
  • 56 Olsen JV, Blagoev B, Gnad F, Macek: B, Kumar C, Mortensen P, Mann M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006;127:635-648.
  • 57 Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol 2006;24:1285-1292.
  • 58 Elias JE, Gygi SP. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods 2007;4:207-214.
  • 59 Hornbeck PV, Chabra I, Kornhauser JM, Skrzypek E, Zhang B. PhosphoSite: a bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics 2004;4:1551-1561.
  • 60 Gnad F, Ren S, Cox J, Olsen JV, Macek B, Oroshi M, Mann M. PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. Genome Biol 2007;8:R250.
 
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