Enrichment strategies in phosphoproteomics

Methods in Molecular Biology

Volumn 1355, Issue , 2016, Pages 105-121

  Leitner, Alexander ^a  

^a NONE

Author keywords

Fractionation; Mass spectrometry; Phosphopeptide enrichment; Sample preparation

Indexed keywords

METAL OXIDE; PHOSPHOPEPTIDE; PHOSPHOPROTEIN;

HUMAN; HYDROPHILIC INTERACTION CHROMATOGRAPHY; IMMOBILIZED METAL AFFINITY CHROMATOGRAPHY; ION EXCHANGE CHROMATOGRAPHY; MASS SPECTROMETRY; PHOSPHOPROTEOMICS; PROTEIN ANALYSIS; PROTEIN PHOSPHORYLATION; PROTEOMICS; AFFINITY CHROMATOGRAPHY; ANIMAL; CHEMICAL PHENOMENA; CHEMISTRY; IMMUNOAFFINITY CHROMATOGRAPHY; IMMUNOLOGY; METABOLISM; PEPTIDE MAPPING; PHOSPHORYLATION; PROCEDURES; PROTEIN PROCESSING; STATIC ELECTRICITY; TANDEM MASS SPECTROMETRY; WORKFLOW;

ANIMALS; CHROMATOGRAPHY, AFFINITY; CHROMATOGRAPHY, ION EXCHANGE; HUMANS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; IMMUNOCHROMATOGRAPHY; PEPTIDE MAPPING; PHOSPHOPROTEINS; PHOSPHORYLATION; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOMICS; STATIC ELECTRICITY; TANDEM MASS SPECTROMETRY; WORKFLOW;

EID: 84947983002     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-3049-4_7     Document Type: Chapter

References (77)

1. Kim M-S, Pinto SM, Getnet D et al (2014) A draft map of the human proteome. Nature 509:575–581
2. Wilhelm M, Schlegl J, Hahne H et al (2014) Mass-spectrometry-based draft of the human proteome. Nature 509:582–587
3. Beltran L, Cutillas PR (2012) Advances in phosphopeptide enrichment techniques for phosphoproteomics. Amino Acids 43:1009–1024
4. Fila J, Honys D (2012) Enrichment techniques employed in phosphoproteomics. Amino Acids 43:1025–1047
5. Engholm-Keller K, Larsen MR (2013) Technologies and challenges in large-scale phosphoproteomics. Proteomics 13:910–931
6. Loroch S, Dickhut C, Zahedi RP, Sickmann A (2013) Phosphoproteomics—More than meets the eye. Electrophoresis 34:1483–1492
7. Guo M, Huang BX (2013) Integration of phosphoproteomic, chemical, and biological strategies for the functional analysis of targeted protein phosphorylation. Proteomics 13: 424–437
8. Roux PP, Thibault P (2013) The coming of age of phosphoproteomics—from large data sets to inference of protein functions. Mol Cell Proteomics 12:3453–3464
9. Jünger MA, Aebersold R (2014) Mass spectrometry- driven phosphoproteomics: patterning the systems biology mosaic. Wiley Interdiscip Rev Dev Biol 3:83–112
10. Wells JM, McLuckey SA (2005) Collisioninduced dissociation (CID) of peptides and proteins. Methods Enzymol 402:148–185
11. Boersema PJ, Mohammed S, Heck AJR (2009) Phosphopeptide fragmentation and analysis by mass spectrometry. J Mass Spectrom 44: 861–878
12. Chalkley RJ, Clauser KR (2012) Modification site localization scoring: strategies and performance. Mol Cell Proteomics 11:3–14
13. Rush J, Moritz A, Lee KA et al (2005) Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat Biotechnol 23: 94–101
14. Boersema PJ, Foong LY, Ding VMY et al (2010) In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling. Mol Cell Proteomics 9:84–99
15. Kee J-M, Oslund RC, Perlman DH et al (2013) A pan-specific antibody for direct detection of protein histidine phosphorylation. Nat Chem Biol 9:416–421
16. Porath J, Carlsson J, Olsson I et al (1975) Metal chelate affinity chromatography, a new approach to protein fractionation. Nature 258:598–599
17. Andersson L, Porath J (1986) Isolation of phosphoproteins by immobilized metal (Fe3+) affinity chromatography. Anal Biochem 154:250–254
18. Zhou H, Ye M, Dong J et al (2008) Specific phosphopeptide enrichment with immobilized titanium ion affinity chromatography adsorbent for phosphoproteome analysis. J Proteome Res 7:3957–3967
19. Zhou H, Ye M, Dong J et al (2013) Robust phosphoproteome enrichment using monodisperse microsphere-based immobilized titanium (IV) ion affinity chromatography. Nat Protoc 8:461–480
20. Iliuk AB, Martin VA, Alicie BM et al (2010) In-depth analyses of kinase-dependent tyrosine phosphoproteomes based on metal ionfunctionalized soluble nanopolymers. Mol Cell Proteomics 9:2162–2172
21. Jayasundera KB, Iliuk AB, Nguyen A et al (2014) Global phosphoproteomics of activated b cells using complementary metal ion functionalized soluble nanopolymers. Anal Chem 86:6363–6371
22. Tsai C-F, Hsu C-C, Hung J-N et al (2014) Sequential phosphoproteomic enrichment through complementary metal-directed immobilized metal ion affinity chromatography. Anal Chem 86:685–693
23. Pinkse MWH, Uitto PM, Hilhorst MJ et al (2004) Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns. Anal Chem 76:3935–3943
24. Larsen MR, Thingholm TE, Jensen ON et al (2005) Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol Cell Proteomics 4:873–886
25. Leitner A (2010) Phosphopeptide enrichment using metal oxide affinity chromatography. Trends Anal Chem 29:177–185
26. Sugiyama N, Masuda T, Shinoda K et al (2007) Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications. Mol Cell Proteomics 6:1103–1109
27. Fukuda I, Hirabayashi-Ishioka Y, Sakikawa I et al (2013) Optimization of enrichment conditions on TiO2 chromatography using glycerol as an additive reagent for effective phosphoproteomic analysis. J Proteome Res 12:5587–5597
28. Kyono Y, Sugiyama N, Imami K et al (2008) Successive and selective release of phosphorylated peptides captured by hydroxy acidmodified metal oxide chromatography. J Proteome Res 7:4585–4593
29. Imami K, Sugiyama N, Kyono Y et al (2008) Automated phosphoproteome analysis for cultured cancer cells by two-dimensional NanoLC-MS using a calcined titania/C18 Biphasic column. Anal Sci 24:161–166
30. Li Q-R, Ning Z-B, Tang J-S et al (2009) Effect of peptide-to-TiO2 beads ratio on phosphopeptide enrichment selectivity. J Proteome Res 8:5375–5381
31. Schmidt A, Trentini DB, Spiess S et al (2014) Quantitative phosphoproteomics reveals the role of protein arginine phosphorylation in the bacterial stress response. Mol Cell Proteomics 13:537–550
32. Beausoleil SA, Jedrychowski M, Schwartz D et al (2004) Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc Natl Acad Sci U S A 101:12130–12135
33. Olsen JV, Blagoev B, Gnad F et al (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127:635–648
34. Han G, Ye M, Zhou H et al (2008) Large-scale phosphoproteome analysis of human liver tissue by enrichment and fractionation of phosphopeptides with strong anion exchange chromatography. Proteomics 8:1346–1361
35. Boersema PJ, Mohammed S, Heck AJR (2008) Hydrophilic interaction liquid chromatography (HILIC) in proteomics. Anal Bioanal Chem 391:151–159
36. McNulty DE, Annan RS (2008) Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection. Mol Cell Proteomics 7:971–980
37. Alpert AJ (2008) Electrostatic repulsion hydrophilic interaction chromatography for isocratic separation of charged solutes and selective isolation of phosphopeptides. Anal Chem 80:62–76
38. Zhang X, Ye J, Jensen ON et al (2007) Highly efficient phosphopeptide enrichment by calcium phosphate precipitation combined with subsequent IMAC enrichment. Mol Cell Proteomics 6:2032–2042
39. Ruse CI, McClatchy DB, Lu B et al (2008) Motif-specific sampling of phosphoproteomes. J Proteome Res 7:2140–2150
40. Güzel Y, Rainer M, Mirza MR et al (2013) Highly selective recovery of phosphopeptides using trypsin-assisted digestion of precipitated lanthanide-phosphoprotein complexes. Analyst 138:2897–2905
41. Leitner A, Lindner W (2009) Chemical tagging strategies for mass spectrometry-based phospho-proteomics. Methods Mol Biol 527:229–243
42. Zhou H, Watts JD, Aebersold R (2001) A systematic approach to the analysis of protein phosphorylation. Nat Biotechnol 19:375–378
43. Tao WA, Wollscheid B, O’Brien R et al (2005) Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nat Methods 2:591–598
44. Nika H, Lee J, Willis IM et al (2012) Phosphopeptide characterization by mass spectrometry using reversed-phase supports for solid-phase β-elimination/michael addition. J Biomol Tech 23:51–68
45. Nika H, Nieves E, Hawke DH et al (2013) Optimization of the β-elimination/michael addition chemistry on reversed-phase supports for mass spectrometry analysis of O-linked protein modifications. J Biomol Tech 24:132–153
46. Fonslow BR, Niessen SM, Singh M et al (2012) Single-step inline hydroxyapatite enrichment facilitates identification and quantitation of phosphopeptides from mass-limited proteomes with MudPIT. J Proteome Res 11:2697–2709
47. 2 O for highly selective capture of phosphopeptides. Sci Rep 4:3753
48. Li X-S, Xu L-D, Zhu G-T et al (2012) Zirconium arsenate-modified magnetic nanoparticles: preparation, characterization and application to the enrichment of phosphopeptides. Analyst 137:959–967
49. 6 : a novel binary affinity probe for global phosphopeptide detection. Chem Commun 49:1762–1764
50. 4 (RE = La, Nd, Eu) affinity nanorods modified on a MALDI plate for rapid capture of target peptides from complex biosamples. Chem Commun 49:8492–8494
51. Cheng G, Liu Y-L, Wang Z-G et al (2013) Yolk-shell magnetic microspheres with mesoporous yttrium phosphate shells for selective capture and identification of phosphopeptides. J Mater Chem B 1:3661–3669
52. Fischnaller M, Köck R, Bakry R et al (2014) Enrichment and desalting of tryptic protein digests and the protein depletion using boron nitride. Anal Chim Acta 823:40–50
53. Furuhashi T, Nukarinen E, Ota S et al (2014) Boron nitride as desalting material in combination with phosphopeptide enrichment in shotgun proteomics. Anal Biochem 452:16–18
54. Li Q-R, Ning Z-B, Yang X-L (2012) Complementary workfl ow for global phosphoproteome analysis. Electrophoresis 33:3291–3298
55. Thingholm TE, Jensen ON, Robinson PJ et al (2008) SIMAC (sequential elution from IMAC), a phosphoproteomics strategy for the rapid separation of monophosphorylated from multiply phosphorylated peptides. Mol Cell Proteomics 7:661–671
56. 2 , SIMAC, and HILIC. J Proteomics 75:5749–5761
57. Mertins P, Qiao JW, Patel J et al (2013) Integrated proteomic analysis of posttranslational modifications by serial enrichment. Nat Methods 10:634–637
58. Swaney DL, Beltrao P, Starita L et al (2013) Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation. Nat Methods 10:676–682
59. Iesmantavicius V, Weinert BT, Choudhary C (2014) Convergence of ubiquitylation and phosphorylation signaling in rapamycin-treated yeast cells. Mol Cell Proteomics 13:1979–1992
60. Beltrao P, Bork P, Krogan NJ et al (2013) Evolution and functional cross-talk of protein post-translational modifications. Mol Syst Biol 9:714
61. Ficarro SB, McCleland ML, Stukenberg PT et al (2002) Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat Biotechnol 20:301–305
62. Zubarev RA, Makarov A (2013) Orbitrap mass spectrometry. Anal Chem 85:5288–5296
63. Hennrich ML, Groenewold V, Kops GJ, Heck AJ et al (2011) Improving depth in phosphoproteomics by using a strong cation exchangeweak anion exchange-reversed phase multidimensional separation approach. Anal Chem 83:7137–7143
64. Hennrich ML, van den Toorn HWP, Groenewold V et al (2012) Ultra acidic strong cation exchange enabling the efficient enrichment of basic phosphopeptides. Anal Chem 84:1804–1808
65. Huttlin EL, Jedrychowski MP, Elias JE et al (2010) A tissue-specific atlas of mouse protein phosphorylation and expression. Cell 143: 1174–1189
66. Lundby A, Secher A, Lage K et al (2012) Quantitative maps of protein phosphorlyation sites across 14 different rat organs and tissues. Nat Commun 3:876
67. Meijer LAT, Zhou H, Chan OYA et al (2013) Quantitative global phosphoproteomics of human umbilical vein endothelial cells after activation of the Rap signaling pathway. Mol Bio Syst 9:732–749
68. Monetti M, Nagaraj N, Sharma K et al (2011) Large-scale phosphosite quantification in tissues by a spike-in SILAC method. Nat Methods 8:655–658
69. Nagaraj N, D’Souza RCJ, Cox J et al (2010) Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation. J Proteome Res 9:6786–6794
70. Olsen JV, Vermeulen M, Santamaria A et al (2010) Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal 3: ra3
71. Phanstiel DH, Brumbaugh J, Wenger CD et al (2011) Proteomic and phosphoproteomic comparison of human ES and iPS cells. Nat Methods 8:821–827
72. Rigbolt KTG, Prokhorova TA, Akimov V et al (2011) System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. Sci Signal 4: rs3
73. Yi T, Zhai B, Yu Y et al (2014) Quantitative phosphoproteomic analysis reveals system-wide signaling pathways downstream of SDF-1/ CXCR4 in breast cancer stem cells. Proc Natl Acad Sci U S A 111:E2182–E2190
74. Yue X-S, Hummon AB (2013) Combination of Multistep IMAC Enrichment with High-pH Reverse Phase Separation for In-Depth Phosphoproteomic Profiling. J Proteome Res 12:4176–4186
75. Zarei M, Sprenger A, Gretzmeier C et al. (2012) Combinatorial Use of Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC) and Strong Cation Exchange (SCX) Chromatography for In-Depth Phosphoproteome Analysis. J Proteome Res 12: 4269–4276
76. Zhou H, Di Palma S, Preisinger C et al. (2013) Toward a Comprehensive Characterization of a Human Cancer Cell Phosphoproteome. J Proteome Res 13:260–271
77. Huang J, Qin H, Dong J et al (2014) In Situ Sample Processing Approach (iSPA) for comprehensive quantitative phosphoproteome analysis. J Proteome Res 13:3896–3904