Hydrophilic strong anion exchange (hSAX) chromatography enables deep fractionation of tissue proteomes

Methods in Molecular Biology

Volumn 1550, Issue , 2017, Pages 69-82

  Ruprecht, Benjamin ^a,b   Wang, Dongxue ^a   Zenezini Chiozzi, Riccardo ^c   Li, Li Hua ^d   Hahne, Hannes ^e   Kuster, Bernhard ^a,b,f  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^b Munich Center for Integrated Protein Science   (Germany)

^c SAPIENZA UNIVERSITY OF ROME   (Italy)

^d TAIPEI VETERANS GENERAL HOSPITAL   (Taiwan)

^e OMICSCOUTS GMBH   (Germany)

^f GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

Chromatography; Deep fractionation; Proteomics; Strong anion exchange; Tissue proteomics

Indexed keywords

DISULFIDE; PROTEOME;

ALKYLATION; AMINO ACID SEQUENCE; ANION EXCHANGE CHROMATOGRAPHY; BRAIN TISSUE; ELECTROSPRAY MASS SPECTROMETRY; FRACTIONATION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; HYDROPHILIC STRONG ANION EXCHANGE CHROMATOGRAPHY; LIQUID CHROMATOGRAPHY-MASS SPECTROMETRY; MASS SPECTROMETER; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN EXPRESSION; REVERSED PHASE LIQUID CHROMATOGRAPHY; TISSUE PREPARATION; TISSUES; CHEMICAL PHENOMENA; ION EXCHANGE CHROMATOGRAPHY; LIQUID CHROMATOGRAPHY; PROCEDURES; PROTEOMICS; SOFTWARE; STATISTICS; TANDEM MASS SPECTROMETRY;

CHEMICAL FRACTIONATION; CHROMATOGRAPHY, ION EXCHANGE; CHROMATOGRAPHY, LIQUID; HUMANS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; PROTEOME; PROTEOMICS; SOFTWARE; STATISTICS AS TOPIC; TANDEM MASS SPECTROMETRY;

EID: 85013001196     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-6747-6_7     Document Type: Chapter

References (24)

1. Wilhelm M, Schlegl J, Hahne H et al (2014) Mass-spectrometry-based draft of the human proteome. Nature 509:582–587
2. Kim M-S, Pinto SM, Getnet D et al (2014) A draft map of the human proteome. Nature 509:575–581
3. Richards AL, Merrill AE, Coon JJ (2015) Proteome sequencing goes deep. Curr Opin Chem Biol 24:11–17
4. Mann M, Kulak NA, Nagaraj N et al (2013) The coming age of complete accurate, and ubiquitous proteomes. Mol Cell 49:583–590
5. Nagaraj N, Wisniewski JR, Geiger T et al (2011) Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol 7:548
6. Beck M, Schmidt A, Malmstroem J et al (2011) The quantitative proteome of a human cell line. Mol Syst Biol 7:549
7. Geiger T, Wehner A, Schaab C et al (2012) Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Mol Cell Proteomics 11:M111.014050
8. Azimifar SB, Nagaraj N, Cox J et al (2014) Cell-type-resolved quantitative proteomics of murine liver. Cell Metab 20:1076–1087
9. Deshmukh AS, Murgia M, Nagaraj N et al (2015) Deep proteomics of mouse skeletal muscle enables quantitation of protein iso-forms, metabolic pathways, and transcription factors. Mol Cell Proteomics 14:841–853
10. Wiśniewski R, Dus-Szachniewicz K, Ostasiewicz P et al (2015) Absolute proteome analysis of colorectal mucosa, adenoma and cancer reveals drastic changes in fatty acid metabolism and plasma membrane transporters. J Proteome Res 14:4005–4018
11. Alpert AJ (1990) Hydrophilic-interaction chromatography for the separation of peptides, nucleic acids and other polar compounds. J Chromatogr 499:177–196
12. Boersema PJ, Divecha N, Heck AJR et al (2007) Evaluation and optimization of ZIC-HILIC-RP as an alternative MudPIT strategy. J Proteome Res 6:937–946
13. Hao P, Guo T, Li X et al (2010) Novel application of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) in shotgun proteomics: comprehensive profiling of rat kidney proteome. J Proteome Res 9:3520–3526
14. Hennrich ML, Groenewold V, Kops GJPL et al (2011) Improving depth in phosphoproteomics by using a strong cation exchange-weak anion exchange-reversed phase multidimensional separation approach. Anal Chem 83:7137–7143
15. Gilar M, Olivova P, Daly AE et al (2005) Two-dimensional separation of peptides using RP-RP-HPLC system with different pH in first and second separation dimensions. J Sep Sci 28:1694–1703
16. Zhou F, Sikorski TW, Ficarro SB et al (2011) Online nanoflow reversed phase-strong anion exchange-reversed phase liquid chromatography-tandem mass spectrometry platform for efficient and in-depth proteome sequence analysis of complex organisms. Anal Chem 83:6996–7005
17. Wolters DA, Washburn MP, Yates JR (2001) An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem 73:5683–5690
18. Ritorto MS, Cook K, Tyagi K et al (2013) Hydrophilic strong anion exchange (hSAX) chromatography for highly orthogonal peptide separation of complex proteomes. J Proteome Res 12:2449–2457
19. Ruprecht B, Koch H, Medard G et al (2015) Comprehensive and reproducible phosphopeptide enrichment using iron immobilized metal ion affinity chromatography (Fe-IMAC) columns. Mol Cell Proteomics 14:205–215
20. 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 26:1367–1372
21. Kulak NA, Pichler G, Paron I et al (2014) Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells. Nat Methods 11:319–324
22. Hahne H, Pachl F, Ruprecht B et al (2013) DMSO enhances electrospray response, boosting sensitivity of proteomic experiments. Nat Methods 10:989–991
23. Cox J, Neuhauser N, Michalski A et al (2011) Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res 10:1794–1805
24. Rappsilber J, Mann M, Ishihama Y (2007) Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc 2:1896–1906