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Mass Spectrometric Analysis of Post-translational Modifications (PTMs) and Protein–Protein Interactions (PPIs)

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Advancements of Mass Spectrometry in Biomedical Research

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 806))

Abstract

Of the 25,000–30,000 human genes, about 2 % code for proteins. However, there are about one to two million protein entities. This is primarily due to alternative splicing and post-translational modifications (PTMs). Identifying all these modifications in one proteome at a particular time point during development or during the transition from normal to cancerous cells is a great challenge to scientists. In addition, identifying the biological significance of all these modifications, as well as their nature, such as stable versus transient modifications, is an even more challenging. Furthermore, interaction of proteins and protein isoforms that have one or more stable or transient PTMs with other proteins and protein isoforms makes the study of proteins daunting and complex. Here we review some of the strategies to study proteins, protein isoforms, protein PTMs, and protein–protein interactions (PPIs). Our goal is to provide a thorough understanding of these proteins and their isoforms, PTMs and PPIs and to shed light on the biological significance of these factors.

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References

  1. Schmutz J et al (2004) Quality assessment of the human genome sequence. Nature 429(6990):365–368

    CAS  Google Scholar 

  2. Stein L (2001) Genome annotation: from sequence to biology. Nat Rev Genet 2(7):493–503

    CAS  Google Scholar 

  3. Eisenberg D et al (2000) Protein function in the post-genomic era. Nature 405(6788):823–826

    CAS  Google Scholar 

  4. Ngounou Wetie AG et al (2013) Investigation of stable and transient protein-protein interactions: past, present and future. Proteomics 13(3–4):538–557

    CAS  Google Scholar 

  5. Ngounou Wetie AG et al (2014) Protein-protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches. Cell Mol Life Sci 71(2):205–228

    CAS  Google Scholar 

  6. Darie C (2013) Investigation of protein-protein interactions by Blue Native-PAGE & mass spectrometry. Mod Chem Appl 1(3):e111

    Google Scholar 

  7. Darie CC, Shetty V, Spellman DS, Zhang G, Xu C, Cardasis HL, Blais S, Fenyo D, Neubert TA (2008) Blue Native PAGE and mass spectrometry analysis of the ephrin stimulation-dependent protein-protein interactions in NG108-EphB2 cells. Applications of mass spectrometry in life safety, NATO science for peace and security series. Springer, Düsseldorf, Germany

    Google Scholar 

  8. Darie CC, Litscher ES, Wassarman PM (2008) Structure, processing, and polymerization of rainbow trout egg vitelline envelope proteins. Applications of mass spectrometry in life safety, NATO science for peace and security series. Springer, Düsseldorf, Germany

    Google Scholar 

  9. Darie CC (2013) Mass spectrometry and its application in life sciences. Aust J Chem 66:1–2

    Google Scholar 

  10. Darie CC et al (2006) Studies of the Ndh complex and photosystem II from mesophyll and bundle sheath chloroplasts of the C4-type plant Zea mays. J Plant Physiol 163(8):800–808

    CAS  Google Scholar 

  11. Darie CC et al (2011) Identifying transient protein-protein interactions in EphB2 signaling by blue native PAGE and mass spectrometry. Proteomics 11(23):4514–4528

    CAS  Google Scholar 

  12. Byrum S et al (2012) Analysis of stable and transient protein-protein interactions. Methods Mol Biol 833:143–152

    CAS  Google Scholar 

  13. Sadrzadeh SM, Bozorgmehr J (2004) Haptoglobin phenotypes in health and disorders. Am J Clin Pathol 121(Suppl):S97–S104

    Google Scholar 

  14. Bashor CJ et al (2010) Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems. Annu Rev Biophys 39:515–537

    CAS  Google Scholar 

  15. McNally FJ, Vale RD (1993) Identification of katanin, an ATPase that severs and disassembles stable microtubules. Cell 75(3):419–429

    CAS  Google Scholar 

  16. Dutcher SK (2001) The tubulin fraternity: alpha to eta. Curr Opin Cell Biol 13(1):49–54

    CAS  Google Scholar 

  17. Hemmerich P, Schmiedeberg L, Diekmann S (2011) Dynamic as well as stable protein interactions contribute to genome function and maintenance. Chromosome Res 19(1):131–151

    CAS  Google Scholar 

  18. Sanderson CM (2008) A new way to explore the world of extracellular protein interactions. Genome Res 18(4):517–520

    CAS  Google Scholar 

  19. DeLano WL (2002) Unraveling hot spots in binding interfaces: progress and challenges. Curr Opin Struct Biol 12(1):14–20

    CAS  Google Scholar 

  20. Krylov D, Mikhailenko I, Vinson C (1994) A thermodynamic scale for leucine zipper stability and dimerization specificity: e and g interhelical interactions. EMBO J 13(12):2849–2861

    CAS  Google Scholar 

  21. Vogelstein B, Lane D, Levine AJ (2000) Surfing the p53 network. Nature 408(6810):307–310

    CAS  Google Scholar 

  22. Ideker T, Sharan R (2008) Protein networks in disease. Genome Res 18(4):644–652

    CAS  Google Scholar 

  23. Schuster-Bockler B, Bateman A (2008) Protein interactions in human genetic diseases. Genome Biol 9(1):R9

    Google Scholar 

  24. Wong JM, Ionescu D, Ingles CJ (2003) Interaction between BRCA2 and replication protein A is compromised by a cancer-predisposing mutation in BRCA2. Oncogene 22(1):28–33

    CAS  Google Scholar 

  25. Jonsson PF, Bates PA (2006) Global topological features of cancer proteins in the human interactome. Bioinformatics 22(18):2291–2297

    CAS  Google Scholar 

  26. Soler-Lopez M et al (2011) Interactome mapping suggests new mechanistic details underlying Alzheimer’s disease. Genome Res 21(3):364–376

    CAS  Google Scholar 

  27. Rikova K et al (2007) Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell 131(6):1190–1203

    CAS  Google Scholar 

  28. Manning G et al (2002) Evolution of protein kinase signaling from yeast to man. Trends Biochem Sci 27(10):514–520

    CAS  Google Scholar 

  29. Deshaies RJ, Joazeiro CA (2009) RING domain E3 ubiquitin ligases. Annu Rev Biochem 78:399–434

    CAS  Google Scholar 

  30. Ohtsubo K, Marth JD (2006) Glycosylation in cellular mechanisms of health and disease. Cell 126(5):855–867

    CAS  Google Scholar 

  31. Olsen JV et al (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127(3):635–648

    CAS  Google Scholar 

  32. Bischoff R, Schluter H (2012) Amino acids: chemistry, functionality and selected non-enzymatic post-translational modifications. J Proteomics 75(8):2275–2296

    CAS  Google Scholar 

  33. Darie C (2013) Mass spectrometry and proteomics: principle, workflow, challenges and perspectives. Mod Chem Appl 1(2):e105

    Google Scholar 

  34. Darie C (2013) Post-translational modification (PTM) proteomics: challenges and perspectives. Mod Chem Appl 1:e114

    Google Scholar 

  35. Ngounou Wetie AG et al (2013) Identification of post-translational modifications by mass spectrometry. Aust J Chem 66:734–748

    Google Scholar 

  36. Ngounou Wetie AG et al (2013) Automated mass spectrometry-based functional assay for the routine analysis of the secretome. J Lab Autom 18(1):19–29

    CAS  Google Scholar 

  37. Ngounou Wetie AG et al (2013) Mass spectrometry for the detection of potential psychiatric biomarkers. J Mol Psychiatry 1:8

    Google Scholar 

  38. Sokolowska I et al (2012) Disulfide proteomics for identification of extracellular or secreted proteins. Electrophoresis 33(16):2527–2536

    CAS  Google Scholar 

  39. Sokolowska I et al (2013) Mass spectrometry investigation of glycosylation on the NXS/T sites in recombinant glycoproteins. Biochim Biophys Acta 1834(8):1474–1483

    CAS  Google Scholar 

  40. Sokolowska I et al (2013) Applications of mass spectrometry in proteomics. Aust J Chem 66:721–733

    CAS  Google Scholar 

  41. Sokolowska I et al (2013) Characterization of tumor differentiation factor (TDF) and its receptor (TDF-R). Cell Mol Life Sci 70(16):2835–2848

    CAS  Google Scholar 

  42. Sokolowska I et al (2011) Mass spectrometry for proteomics-based investigation of oxidative stress and heat shock proteins. In: Andreescu S, Hepel M (eds) Oxidative stress: diagnostics, prevention, and therapy. American Chemical Society, Washington, DC

    Google Scholar 

  43. Woods AG, Sokolowska I, Darie CC (2012) Identification of consistent alkylation of cysteine-less peptides in a proteomics experiment. Biochem Biophys Res Commun 419(2):305–308

    CAS  Google Scholar 

  44. Woods AG et al (2012) Potential biomarkers in psychiatry: focus on the cholesterol system. J Cell Mol Med 16(6):1184–1195

    CAS  Google Scholar 

  45. Woods AG et al (2011) Blue native page and mass spectrometry as an approach for the investigation of stable and transient protein-protein interactions. In: Andreescu S, Hepel M (eds) Oxidative stress: diagnostics, prevention, and therapy. American Chemical Society, Washington, DC

    Google Scholar 

  46. Olsen JV et al (2010) Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal 3(104):ra3

    Google Scholar 

  47. Zhang G et al (2006) Quantitative phosphotyrosine proteomics of EphB2 signaling by stable isotope labeling with amino acids in cell culture (SILAC). J Proteome Res 5(3):581–588

    CAS  Google Scholar 

  48. Rinschen MM et al (2010) Quantitative phosphoproteomic analysis reveals vasopressin V2-receptor-dependent signaling pathways in renal collecting duct cells. Proc Natl Acad Sci U S A 107(8):3882–3887

    CAS  Google Scholar 

  49. Cantin GT et al (2006) Quantitative phosphoproteomic analysis of the tumor necrosis factor pathway. J Proteome Res 5(1):127–134

    CAS  Google Scholar 

  50. Hanahan D, Weinberg RA (2000) The hallmarks of cancer. Cell 100(1):57–70

    CAS  Google Scholar 

  51. Pan C et al (2009) Comparative proteomic phenotyping of cell lines and primary cells to assess preservation of cell type-specific functions. Mol Cell Proteomics 8(3):443–450

    CAS  Google Scholar 

  52. Lee J et al (2006) Tumor stem cells derived from glioblastomas cultured in bFGF and EGF more closely mirror the phenotype and genotype of primary tumors than do serum-cultured cell lines. Cancer Cell 9(5):391–403

    CAS  Google Scholar 

  53. Malik R et al (2010) From proteome lists to biological impact—tools and strategies for the analysis of large MS data sets. Proteomics 10(6):1270–1283

    CAS  Google Scholar 

  54. Finkel T (2011) Signal transduction by reactive oxygen species. J Cell Biol 194(1):7–15

    CAS  Google Scholar 

  55. Hill BG et al (2010) What part of NO don’t you understand? Some answers to the cardinal questions in nitric oxide biology. J Biol Chem 285(26):19699–19704

    CAS  Google Scholar 

  56. Higdon A et al (2012) Cell signalling by reactive lipid species: new concepts and molecular mechanisms. Biochem J 442(3):453–464

    CAS  Google Scholar 

  57. Pacher P, Beckman JS, Liaudet L (2007) Nitric oxide and peroxynitrite in health and disease. Physiol Rev 87(1):315–424

    CAS  Google Scholar 

  58. Apweiler R, Hermjakob H, Sharon N (1999) On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database. Biochim Biophys Acta 1473(1):4–8

    CAS  Google Scholar 

  59. Kornfeld R, Kornfeld S (1985) Assembly of asparagine-linked oligosaccharides. Annu Rev Biochem 54:631–664

    CAS  Google Scholar 

  60. Stanley P (2011) Golgi glycosylation. Cold Spring Harb Perspect Biol 3(4):1–13

    Google Scholar 

  61. Halim A et al (2011) Site-specific characterization of threonine, serine, and tyrosine glycosylations of amyloid precursor protein/amyloid beta-peptides in human cerebrospinal fluid. Proc Natl Acad Sci U S A 108(29):11848–11853

    CAS  Google Scholar 

  62. Steentoft C et al (2011) Mining the O-glycoproteome using zinc-finger nuclease-glycoengineered SimpleCell lines. Nat Methods 8(11):977–982

    CAS  Google Scholar 

  63. Spiro RG (1969) Characterization and quantitative determination of the hydroxylysine-linked carbohydrate units of several collagens. J Biol Chem 244(4):602–612

    CAS  Google Scholar 

  64. Spiro RG (2002) Protein glycosylation: nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds. Glycobiology 12(4):43R–56R

    CAS  Google Scholar 

  65. Reis CA et al (2010) Alterations in glycosylation as biomarkers for cancer detection. J Clin Pathol 63(4):322–329

    CAS  Google Scholar 

  66. Aggarwal S (2010) What’s fueling the biotech engine—2009-2010. Nat Biotechnol 28(11):1165–1171

    CAS  Google Scholar 

  67. Hunt JV, Dean RT, Wolff SP (1988) Hydroxyl radical production and autoxidative glycosylation. Glucose autoxidation as the cause of protein damage in the experimental glycation model of diabetes mellitus and ageing. Biochem J 256(1):205–212

    CAS  Google Scholar 

  68. Smith MA et al (1994) Advanced Maillard reaction end products, free radicals, and protein oxidation in Alzheimer’s disease. Ann N Y Acad Sci 738:447–454

    CAS  Google Scholar 

  69. Elsholz AK et al (2012) Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis. Proc Natl Acad Sci U S A 109(19):7451–7456

    CAS  Google Scholar 

  70. Laub MT, Goulian M (2007) Specificity in two-component signal transduction pathways. Annu Rev Genet 41:121–145

    CAS  Google Scholar 

  71. Barford D (1996) Molecular mechanisms of the protein serine/threonine phosphatases. Trends Biochem Sci 21(11):407–412

    CAS  Google Scholar 

  72. Zhang ZY (2002) Protein tyrosine phosphatases: structure and function, substrate specificity, and inhibitor development. Annu Rev Pharmacol Toxicol 42:209–234

    CAS  Google Scholar 

  73. Johnson LN, Barford D (1993) The effects of phosphorylation on the structure and function of proteins. Annu Rev Biophys Biomol Struct 22:199–232

    CAS  Google Scholar 

  74. Hunter T (2007) The age of crosstalk: phosphorylation, ubiquitination, and beyond. Mol Cell 28(5):730–738

    CAS  Google Scholar 

  75. Braconi Quintaje S, Orchard S (2008) The annotation of both human and mouse kinomes in UniProtKB/Swiss-Prot: one small step in manual annotation, one giant leap for full comprehension of genomes. Mol Cell Proteomics 7(8):1409–1419

    Google Scholar 

  76. Jackson MD, Denu JM (2001) Molecular reactions of protein phosphatases—insights from structure and chemistry. Chem Rev 101(8):2313–2340

    CAS  Google Scholar 

  77. Guan KL, Dixon JE (1991) Evidence for protein-tyrosine-phosphatase catalysis proceeding via a cysteine-phosphate intermediate. J Biol Chem 266(26):17026–17030

    CAS  Google Scholar 

  78. Paik WK, Paik DC, Kim S (2007) Historical review: the field of protein methylation. Trends Biochem Sci 32(3):146–152

    CAS  Google Scholar 

  79. Ishikawa Y, Melville DB (1970) The enzymatic alpha-N-methylation of histidine. J Biol Chem 245(22):5967–5973

    CAS  Google Scholar 

  80. Bedford MT, Clarke SG (2009) Protein arginine methylation in mammals: who, what, and why. Mol Cell 33(1):1–13

    CAS  Google Scholar 

  81. Wang C et al (2005) A general fluorescence-based coupled assay for S-adenosylmethionine-dependent methyltransferases. Biochem Biophys Res Commun 331(1):351–356

    CAS  Google Scholar 

  82. Erce MA et al (2012) The methylproteome and the intracellular methylation network. Proteomics 12(4–5):564–586

    CAS  Google Scholar 

  83. Darwanto A et al (2010) A modified “cross-talk” between histone H2B Lys-120 ubiquitination and H3 Lys-79 methylation. J Biol Chem 285(28):21868–21876

    CAS  Google Scholar 

  84. Haglund K, Dikic I (2005) Ubiquitylation and cell signaling. EMBO J 24(19):3353–3359

    CAS  Google Scholar 

  85. Pickart CM, Eddins MJ (2004) Ubiquitin: structures, functions, mechanisms. Biochim Biophys Acta 1695(1–3):55–72

    CAS  Google Scholar 

  86. Nijman SM et al (2005) A genomic and functional inventory of deubiquitinating enzymes. Cell 123(5):773–786

    CAS  Google Scholar 

  87. Bhoj VG, Chen ZJ (2009) Ubiquitylation in innate and adaptive immunity. Nature 458(7237):430–437

    CAS  Google Scholar 

  88. Manning G et al (2002) The protein kinase complement of the human genome. Science 298(5600):1912–1934

    CAS  Google Scholar 

  89. Alonso A et al (2004) Protein tyrosine phosphatases in the human genome. Cell 117(6):699–711

    CAS  Google Scholar 

  90. Shi Y (2009) Serine/threonine phosphatases: mechanism through structure. Cell 139(3):468–484

    CAS  Google Scholar 

  91. Danielsen JM et al (2011) Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. Mol Cell Proteomics 10(3):M110.003590

    Google Scholar 

  92. Jin L et al (2012) Ubiquitin-dependent regulation of COPII coat size and function. Nature 482(7386):495–500

    CAS  Google Scholar 

  93. Pickart CM (2001) Mechanisms underlying ubiquitination. Annu Rev Biochem 70:503–533

    CAS  Google Scholar 

  94. Motegi A et al (2008) Polyubiquitination of proliferating cell nuclear antigen by HLTF and SHPRH prevents genomic instability from stalled replication forks. Proc Natl Acad Sci U S A 105(34):12411–12416

    CAS  Google Scholar 

  95. Zhao S et al (2010) Regulation of cellular metabolism by protein lysine acetylation. Science 327(5968):1000–1004

    CAS  Google Scholar 

  96. Wellen KE et al (2009) ATP-citrate lyase links cellular metabolism to histone acetylation. Science 324(5930):1076–1080

    CAS  Google Scholar 

  97. Ganesan A et al (2009) Epigenetic therapy: histone acetylation, DNA methylation and anti-cancer drug discovery. Curr Cancer Drug Targets 9(8):963–981

    CAS  Google Scholar 

  98. Li G, Reinberg D (2011) Chromatin higher-order structures and gene regulation. Curr Opin Genet Dev 21(2):175–186

    CAS  Google Scholar 

  99. Khan SN, Khan AU (2010) Role of histone acetylation in cell physiology and diseases: an update. Clin Chim Acta 411(19–20):1401–1411

    CAS  Google Scholar 

  100. Sato N et al (2003) Frequent hypomethylation of multiple genes overexpressed in pancreatic ductal adenocarcinoma. Cancer Res 63(14):4158–4166

    CAS  Google Scholar 

  101. Balasubramanyam K et al (2004) Curcumin, a novel p300/CREB-binding protein-specific inhibitor of acetyltransferase, represses the acetylation of histone/nonhistone proteins and histone acetyltransferase-dependent chromatin transcription. J Biol Chem 279(49):51163–51171

    CAS  Google Scholar 

  102. Aggarwal S et al (2006) Curcumin (diferuloylmethane) down-regulates expression of cell proliferation and antiapoptotic and metastatic gene products through suppression of IkappaBalpha kinase and Akt activation. Mol Pharmacol 69(1):195–206

    CAS  Google Scholar 

  103. Choudhary C et al (2009) Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325(5942):834–840

    CAS  Google Scholar 

  104. Plazas-Mayorca MD et al (2010) Quantitative proteomics reveals direct and indirect alterations in the histone code following methyltransferase knockdown. Mol Biosyst 6(9):1719–1729

    CAS  Google Scholar 

  105. Sokolowska I et al (2012) Proteomic analysis of plasma membranes isolated from undifferentiated and differentiated HepaRG cells. Proteome Sci 10(1):47

    CAS  Google Scholar 

  106. Sokolowska I et al (2013) The potential of biomarkers in psychiatry: focus on proteomics. J Neural Transm 1–10)

    Google Scholar 

  107. Woods AG et al (2013) Mass spectrometry as a tool for studying autism spectrum disorder. J Mol Psychiatry 1:6

    Google Scholar 

  108. Garcia BA (2010) What does the future hold for top down mass spectrometry? J Am Soc Mass Spectrom 21(2):193–202

    CAS  Google Scholar 

  109. Cannon J et al (2010) High-throughput middle-down analysis using an orbitrap. J Proteome Res 9(8):3886–3890

    CAS  Google Scholar 

  110. Picotti P, Aebersold R (2012) Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat Methods 9(6):555–566

    CAS  Google Scholar 

  111. Lehmann WD et al (2007) Neutral loss-based phosphopeptide recognition: a collection of caveats. J Proteome Res 6(7):2866–2873

    CAS  Google Scholar 

  112. Syka JE et al (2004) Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci U S A 101(26):9528–9533

    CAS  Google Scholar 

  113. Kelleher NL et al (1999) Localization of labile posttranslational modifications by electron capture dissociation: the case of gamma-carboxyglutamic acid. Anal Chem 71(19):4250–4253

    CAS  Google Scholar 

  114. Good DM et al (2007) Performance characteristics of electron transfer dissociation mass spectrometry. Mol Cell Proteomics 6(11):1942–1951

    CAS  Google Scholar 

  115. Choudhary C, Mann M (2010) Decoding signalling networks by mass spectrometry-based proteomics. Nat Rev Mol Cell Biol 11(6):427–439

    CAS  Google Scholar 

  116. Fields S, Song O (1989) A novel genetic system to detect protein-protein interactions. Nature 340(6230):245–246

    CAS  Google Scholar 

  117. Monti M et al (2005) Interaction proteomics. Biosci Rep 25(1–2):45–56

    CAS  Google Scholar 

  118. Miernyk JA, Thelen JJ (2008) Biochemical approaches for discovering protein-protein interactions. Plant J 53(4):597–609

    CAS  Google Scholar 

  119. Berkowitz SA (2006) Role of analytical ultracentrifugation in assessing the aggregation of protein biopharmaceuticals. AAPS J 8(3):E590–E605

    CAS  Google Scholar 

  120. Miyashita T (2004) Confocal microscopy for intracellular co-localization of proteins. Methods Mol Biol 261:399–410

    CAS  Google Scholar 

  121. Berggard T, Linse S, James P (2007) Methods for the detection and analysis of protein-protein interactions. Proteomics 7(16):2833–2842

    Google Scholar 

  122. Jensen ON (2006) Interpreting the protein language using proteomics. Nat Rev Mol Cell Biol 7(6):391–403

    CAS  Google Scholar 

  123. Schagger H, von Jagow G (1991) Blue native electrophoresis for isolation of membrane protein complexes in enzymatically active form. Anal Biochem 199(2):223–231

    CAS  Google Scholar 

  124. Schagger H, Cramer WA, von Jagow G (1994) Analysis of molecular masses and oligomeric states of protein complexes by blue native electrophoresis and isolation of membrane protein complexes by two-dimensional native electrophoresis. Anal Biochem 217(2):220–230

    CAS  Google Scholar 

  125. Darie CC et al (2005) Isolation and structural characterization of the Ndh complex from mesophyll and bundle sheath chloroplasts of Zea mays. FEBS J 272(11):2705–2716

    CAS  Google Scholar 

  126. Spellman DS et al (2008) Stable isotopic labeling by amino acids in cultured primary neurons: application to brain-derived neurotrophic factor-dependent phosphotyrosine-associated signaling. Mol Cell Proteomics 7(6):1067–1076

    CAS  Google Scholar 

  127. Schagger H (1995) Native electrophoresis for isolation of mitochondrial oxidative phosphorylation protein complexes. Methods Enzymol 260:190–202

    CAS  Google Scholar 

  128. Ganem J, Li YT, Henion J (1991) Detection of noncovalent receptor-ligand complexes by mass spectrometry. J Am Chem Soc 113:6294–6296

    CAS  Google Scholar 

  129. Sakata E et al (2011) The catalytic activity of Ubp6 enhances maturation of the proteasomal regulatory particle. Mol Cell 42(5):637–649

    CAS  Google Scholar 

  130. Zhou M et al (2008) Mass spectrometry reveals modularity and a complete subunit interaction map of the eukaryotic translation factor eIF3. Proc Natl Acad Sci U S A 105(47):18139–18144

    CAS  Google Scholar 

  131. Lorenzen K et al (2007) Structural biology of RNA polymerase III: mass spectrometry elucidates subcomplex architecture. Structure 15(10):1237–1245

    CAS  Google Scholar 

  132. Uetrecht C et al (2008) High-resolution mass spectrometry of viral assemblies: molecular composition and stability of dimorphic hepatitis B virus capsids. Proc Natl Acad Sci U S A 105(27):9216–9220

    CAS  Google Scholar 

  133. Barrera NP et al (2008) Micelles protect membrane complexes from solution to vacuum. Science 321(5886):243–246

    CAS  Google Scholar 

  134. Barrera NP et al (2009) Mass spectrometry of membrane transporters reveals subunit stoichiometry and interactions. Nat Methods 6(8):585–587

    CAS  Google Scholar 

  135. Xie F et al (2011) Liquid chromatography-mass spectrometry-based quantitative proteomics. J Biol Chem 286(29):25443–25449

    CAS  Google Scholar 

  136. Filiou MD et al (2012) To label or not to label: applications of quantitative proteomics in neuroscience research. Proteomics 12(4–5):736–747

    CAS  Google Scholar 

  137. Mann M (2006) Functional and quantitative proteomics using SILAC. Nat Rev Mol Cell Biol 7(12):952–958

    CAS  Google Scholar 

  138. Gygi SP et al (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17(10):994–999

    CAS  Google Scholar 

  139. Ross PL et al (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3(12):1154–1169

    CAS  Google Scholar 

  140. Ong SE et al (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1(5):376–386

    CAS  Google Scholar 

  141. Oeljeklaus S, Meyer HE, Warscheid B (2009) New dimensions in the study of protein complexes using quantitative mass spectrometry. FEBS Lett 583(11):1674–1683

    CAS  Google Scholar 

  142. Foster LJ et al (2006) Insulin-dependent interactions of proteins with GLUT4 revealed through stable isotope labeling by amino acids in cell culture (SILAC). J Proteome Res 5(1):64–75

    CAS  Google Scholar 

  143. Dobreva I et al (2008) Mapping the integrin-linked kinase interactome using SILAC. J Proteome Res 7(4):1740–1749

    CAS  Google Scholar 

  144. Trinkle-Mulcahy L et al (2006) Repo-Man recruits PP1 gamma to chromatin and is essential for cell viability. J Cell Biol 172(5):679–692

    CAS  Google Scholar 

  145. Blagoev B et al (2003) A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat Biotechnol 21(3):315–318

    CAS  Google Scholar 

  146. Pflieger D et al (2008) Quantitative proteomic analysis of protein complexes: concurrent identification of interactors and their state of phosphorylation. Mol Cell Proteomics 7(2):326–346

    CAS  Google Scholar 

  147. Knight ZA et al (2003) Phosphospecific proteolysis for mapping sites of protein phosphorylation. Nat Biotechnol 21(9):1047–1054

    CAS  Google Scholar 

  148. Oda Y, Nagasu T, Chait BT (2001) Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat Biotechnol 19(4):379–382

    CAS  Google Scholar 

  149. Wells L et al (2002) Mapping sites of O-GlcNAc modification using affinity tags for serine and threonine post-translational modifications. Mol Cell Proteomics 1(10):791–804

    CAS  Google Scholar 

  150. Li W et al (2003) Susceptibility of the hydroxyl groups in serine and threonine to beta-elimination/Michael addition under commonly used moderately high-temperature conditions. Anal Biochem 323(1):94–102

    CAS  Google Scholar 

  151. Dephoure N et al (2008) A quantitative atlas of mitotic phosphorylation. Proc Natl Acad Sci U S A 105(31):10762–10767

    CAS  Google Scholar 

  152. Tan CS et al (2009) Positive selection of tyrosine loss in metazoan evolution. Science 325(5948):1686–1688

    CAS  Google Scholar 

  153. Zhang K et al (2004) Differentiation between peptides containing acetylated or tri-methylated lysines by mass spectrometry: an application for determining lysine 9 acetylation and methylation of histone H3. Proteomics 4(1):1–10

    CAS  Google Scholar 

  154. Toda T et al (2010) Proteomic approaches to oxidative protein modifications implicated in the mechanism of aging. Geriatr Gerontol Int 10(Suppl 1):S25–S31

    Google Scholar 

  155. Lapko VN, Smith DL, Smith JB (2000) Identification of an artifact in the mass spectrometry of proteins derivatized with iodoacetamide. J Mass Spectrom 35(4):572–575

    CAS  Google Scholar 

  156. Lundell N, Schreitmuller T (1999) Sample preparation for peptide mapping—a pharmaceutical quality-control perspective. Anal Biochem 266(1):31–47

    CAS  Google Scholar 

  157. Windsor WT et al (1993) Disulfide bond assignments and secondary structure analysis of human and murine interleukin 10. Biochemistry 32(34):8807–8815

    CAS  Google Scholar 

  158. Yang Z, Attygalle AB (2007) LC/MS characterization of undesired products formed during iodoacetamide derivatization of sulfhydryl groups of peptides. J Mass Spectrom 42(2):233–243

    CAS  Google Scholar 

  159. Michalski A, Cox J, Mann M (2011) More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J Proteome Res 10(4):1785–1793

    CAS  Google Scholar 

  160. Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26(12):1367–1372

    CAS  Google Scholar 

  161. Wu R et al (2011) A large-scale method to measure absolute protein phosphorylation stoichiometries. Nat Methods 8(8):677–683

    CAS  Google Scholar 

  162. Kool J et al (2011) Studying protein-protein affinity and immobilized ligand-protein affinity interactions using MS-based methods. Anal Bioanal Chem 401(4):1109–1125

    CAS  Google Scholar 

  163. Bunt J et al (2012) OTX2 directly activates cell cycle genes and inhibits differentiation in medulloblastoma cells. Int J Cancer 131(2):E21–E32

    CAS  Google Scholar 

  164. Brewis IA, Brennan P (2010) Proteomics technologies for the global identification and quantification of proteins. Adv Protein Chem Struct Biol 80:1–44

    CAS  Google Scholar 

  165. Wang F, Pan YC (1991) Structural analyses of proteins electroblotted from native polyacrylamide gels onto polyvinyldiene difluoride membranes. A method for determining the stoichiometry of protein-protein interaction in solution. Anal Biochem 198(2):285–291

    CAS  Google Scholar 

  166. Wang F et al (1993) Electroblotting proteolytic products from native gel for direct N-terminal sequence analysis: an approach for studying protein-protein interaction. Electrophoresis 14(9):847–851

    CAS  Google Scholar 

  167. Karger BL, Chu YH, Foret F (1995) Capillary electrophoresis of proteins and nucleic acids. Annu Rev Biophys Biomol Struct 24:579–610

    CAS  Google Scholar 

  168. Vergnon AL, Chu YH (1999) Electrophoretic methods for studying protein-protein interactions. Methods 19(2):270–277

    CAS  Google Scholar 

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Acknowledgments

We would like to thank Ms. Laura Mulderig, Scott Nichols, and their colleagues (Waters Corporation) for their generous support in setting up the Proteomics Center at Clarkson University. C.C.D. thanks Drs. Thomas A. Neubert (New York University), Belinda Willard (Cleveland Clinic), and Gregory Wolber and David Mclaughin (Eastman Kodak Company) for donation of a TofSpec2E MALDI-MS (each). This work was supported in part by the Keep a Breast Foundation (KEABF-375-35054), the Redcay Foundation (SUNY Plattsburgh), the Alexander von Humboldt Foundation, SciFund Challenge, private donations (Ms. Mary Stewart Joyce, Mr. Kenneth Sandler, Bob Mattloff), and by the U.S. Army research office (DURIP grant #W911NF-11-1-0304).

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  1. Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699-5810, USA

    Armand G. Ngounou Wetie, Alisa G. Woods & Costel C. Darie

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  1. Armand G. Ngounou Wetie
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  2. Alisa G. Woods
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  3. Costel C. Darie
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Correspondence to Costel C. Darie .

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  1. Chemistry and Biomolecular Science Biochemistry and Proteomics Group, Clarkson University, Potsdam, New York, USA

    Alisa G. Woods

  2. Chemistry and Biomolecular Science Biochemistry and Proteomics Group, Clarkson University, Potsdam, New York, USA

    Costel C. Darie

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Wetie, A.G.N., Woods, A.G., Darie, C.C. (2014). Mass Spectrometric Analysis of Post-translational Modifications (PTMs) and Protein–Protein Interactions (PPIs). In: Woods, A., Darie, C. (eds) Advancements of Mass Spectrometry in Biomedical Research. Advances in Experimental Medicine and Biology, vol 806. Springer, Cham. https://doi.org/10.1007/978-3-319-06068-2_9

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