Separation with zwitterionic hydrophilic interaction liquid chromatography improves protein identification by matrix-assisted laser desorption/ionization-based proteomic analysis

Biomedical Chromatography

Volumn 23, Issue 6, 2009, Pages 607-614

  Intoh, Atsushi ^a   Kurisaki, Akira ^b   Fukuda, Hiroyuki ^c,d   Asashima, Makoto ^a,b,e  

^a UNIVERSITY OF TOKYO   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c THE UNIVERSITY OF TOKYO   (Japan)

^d Theravalues Corporation   (Japan)

^e Japan USA Organ Regeneration Project   (Japan)

Author keywords

iTRAQ; MALDI TOF MS; Proteomics; Strong cation exchange chromatography; ZIC HILIC

Indexed keywords

CELL MEMBRANES; DESORPTION; HYDROPHILICITY; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MOLECULAR BIOLOGY; POSITIVE IONS; STEM CELLS;

CATION EXCHANGE CHROMATOGRAPHY; HYDROPHILIC INTERACTION LIQUID CHROMATOGRAPHIES; ITRAQ; MALDI-TOF MASS SPECTROMETRY; MASS SPECTROMETRY ANALYSIS; PROTEOMICS; STRONG CATION EXCHANGE CHROMATOGRAPHY; STRONG CATION EXCHANGES; ZWITTERIONIC HYDROPHILIC INTERACTION LIQUID CHROMATOGRAPHY; ZWITTERIONICS;

PEPTIDES;

CELL SURFACE MARKER; HUMAN SERUM ALBUMIN; MEMBRANE PROTEIN; PEPTIDE; TRYPSIN; SERUM ALBUMIN;

ANIMAL CELL; ANIMAL CELL CULTURE; ARTICLE; CATION EXCHANGE; CELL DIFFERENTIATION; CELL LINE; CONTROLLED STUDY; EMBRYONIC STEM CELL; FRACTIONATION; HYDROPHILICITY; LIQUID CHROMATOGRAPHY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOUSE; NONHUMAN; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEOMICS; QUANTITATIVE ANALYSIS; SEPARATION TECHNIQUE; ZWITTERIONIC HYDROPHILIC INTERACTION LIQUID CHROMATOGRAPHY; ANIMAL; CHEMISTRY; CYTOLOGY; EVALUATION; HUMAN; ION EXCHANGE CHROMATOGRAPHY; ISOLATION AND PURIFICATION; MASS SPECTROMETRY; METABOLISM; METHODOLOGY;

ANIMALS; CELL LINE; CHROMATOGRAPHY, ION EXCHANGE; EMBRYONIC STEM CELLS; HUMANS; MEMBRANE PROTEINS; MICE; PEPTIDES; PROTEOMICS; SERUM ALBUMIN; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TRYPSIN;

EID: 67651219584     PISSN: 02693879     EISSN: 10990801     Source Type: Journal    
DOI: 10.1002/bmc.1159     Document Type: Article

References (47)

1. Beavis RC and Chait BT. Matrix-assisted laser desorption ionization mass-spectrometry of proteins. Methods in Enzymology 1996; 270: 519-551.
2. Boersema PJ, Divecha N, Heck AJ and Mohammed S. Evaluation and optimization of ZIC-HILIC-RP as an alternative MudPIT strategy. Journal of Proteome Research 2007; 6: 937-946.
3. Briseno Marroquin B, Wolter D and Willershausen-Zonnchen B. Dimensional variability of nonstandardized greater taper finger spreaders with matching gutta-percha points. International Endodontic Journal 2001; 34: 23-28.
4. Choe LH, Aggarwal K, Franck Z and Lee KH. A comparison of the consistency of proteome quantitation using two-dimensional electrophoresis and shotgun isobaric tagging in Escherichia coli cells. Electrophoresis 2005; 26: 2437-2449.
5. Corthals GL, Wasinger VC, Hochstrasser DF and Sanchez JC. The dynamic range of protein expression: a challenge for proteomic research. Electrophoresis 2000; 21: 1104-1115.
6. Davis MT, Beierle J, Bures ET, McGinley MD, Mort J, Robinson JH, Spahr CS, Yu W, Luethy R and Patterson SD. Automated LC-LC-MS-MS platform using binary ion-exchange and gradient reversed-phase chromatography for improved proteomic analyses. Journal of Chromatography B: Biomedical Sciences and Applications 2001; 752: 281-291.
7. Dell'Aversano C, Eaglesham GK and Quilliam MA. Analysis of cyanobacterial toxins by hydrophilic interaction liquid chromatographymass spectrometry. Journal of Chromatography A 2004; 1028: 155-164.
8. DeSouza L, Diehl G, Rodrigues MJ, Guo J, Romaschin AD, Colgan TJ and Siu KW. Search for cancer markers from endometrial tissues using differentially labeled tags iTRAQ and cICAT with multidimensional liquid chromatography and tandem mass spectrometry. Journal of Proteome Research 2005; 4: 377-386.
9. Diener M, Erler K, Christian B and Luckas B. Application of a new zwitterionic hydrophilic interaction chromatography column for determination of paralytic shellfish poisoning toxins. Journal of Separation Science 2007; 30: 1821-1826.
10. Fernandez-de-Cossio J, Gonzalez J, Betancourt L, Besada V, Padron G, Shimonishi Y and Takao T. Automated interpretation of high-energy collision-induced dissociation spectra of singly protonated peptides by 'SeqMS', a software aid for de novo sequencing by tandem mass spectrometry. Rapid Communications in Mass Spectrometry 1998; 12: 1867-1878.
11. Gorg A, Obermaier C, Boguth G, Harder A, Scheibe B, Wildgruber R and Weiss W. The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 2000; 21: 1037-1053.
12. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH and Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnology 1999; 17: 994-999.
13. Hagglund P, Bunkenborg J, Elortza F, Jensen ON and Roepstorff P. A new strategy for identification of N-glycosylated proteins and unambiguous assignment of their glycosylation sites using HILIC enrichment and partial deglycosylation. Journal of Proteome Research 2004; 3: 556-566.
14. Hardt M, Witkowska HE, Webb S, Thomas LR, Dixon SE, Hall SC and Fisher SJ. Assessing the effects of diurnal variation on the composition of human parotid saliva: quantitative analysis of native peptides using iTRAQ reagents. Analytical Chemistry 2005; 77: 4947-4954.
15. Hopkins AL and Groom CR. The druggable genome. Nature Reviews. Drug Discovery 2002; 1: 727-730.
16. Ichibangase T, Moriya K, Koike K and Imai K. A proteomics method revealing disease-related proteins in livers of hepatitis-infected mouse model. Journal of Proteome Research 2007; 6: 2841-2849.
17. Idborg H, Zamani L, Edlund PO, Schuppe-Koistinen I and Jacobsson SP. Metabolic fingerprinting of rat urine by LC/MS Part 1. Analysis by hydrophilic interaction liquid chromatography-electrospray ionization mass spectrometry. Journal of Chromatography B, Analytical Technologies in the Biomedical and Life Sciences 2005a; 828: 9-13.
18. Idborg H, Zamani L, Edlund PO, Schuppe-Koistinen I and Jacobsson SP. Metabolic fingerprinting of rat urine by LC/MS Part 2. Data pretreatment methods for handling of complex data. Journal of Chromatography B, Analytical Technologies in the Biomedical and Life Sciences 2005b; 828: 14-20.
19. Jiang W and Irgum K. Synthesis and evaluation of polymer-based zwitterionic stationary phases for separation of ionic species. Analytical Chemistry 2001; 73: 1993-2003.
20. Jiang X, Feng S, Tian R, Han G, Ye M and Zou H. Automation of nanoflow liquid chromatography-tandem mass spectrometry for proteome analysis by using a strong cation exchange trap column. Proteomics 2007; 7: 528-539.
21. Klein C, Garcia-Rizo C, Bisle B, Scheffer B, Zischka H, Pfeiffer F, Siedler F and Oesterhelt D. The membrane proteome of Halobacterium salinarum. Proteomics 2005; 5: 180-197.
22. Kolkman A, Dirksen EH, Slijper M and Heck AJ. Double standards in quantitative proteomics: direct comparative assessment of difference in gel electrophoresis and metabolic stable isotope labeling. Molecular and Cellular Proteomics 2005; 4: 255-266.
23. Litowski JR, Semchuk PD, Mant CT and Hodges RS. Hydrophilic interaction/ cation-exchange chromatography for the purification of synthetic peptides from closely related impurities: serine side-chain acetylated peptides. Journal of Peptide Research 1999; 54: 1-11.
24. Lopez MF. Better approaches to finding the needle in a haystack: optimizing proteome analysis through automation. Electrophoresis 2000; 21: 1082-1093.
25. Nagano K, Taoka M, Yamauchi Y, Itagaki C, Shinkawa T, Nunomura K, Okamura N, Takahashi N, Izumi T and Isobe T. Large-scale identification of proteins expressed in mouse embryonic stem cells. Proteomics 2005; 5: 1346-1361.
26. Ogino T, Fukuda H, Imajoh-Ohmi S, Kohara M and Nomoto A. Membrane binding properties and terminal residues of the mature hepatitis C virus capsid protein in insect cells. Journal of Virology 2004; 78: 11766-11777.
27. Pandey A and Mann M. Proteomics to study genes and genomes. Nature 2000; 405: 837-846.
28. Peng J, Elias JE, Thoreen CC, Licklider LJ and Gygi SP. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. Journal of Proteome Research 2003; 2: 43-50.
29. Pieper R, Gatlin CL, Makusky AJ, Russo PS, Schatz CR, Miller SS, Su Q, McGrath AM, Estock MA, Parmar PP, Zhao M, Huang ST, Zhou J, Wang F, Esquer-Blasco R, Anderson NL, Taylor J and Steiner S. The human serum proteome: display of nearly 3700 chromatographically separated protein spots on two-dimensional electrophoresis gels and identification of 325 distinct proteins. Proteomics 2003; 3: 1345-1364.
30. Pistos C, Tsantili-Kakoulidou A and Koupparis M. Investigation of the retention/pH profile of zwitterionic fluoroquinolones in reversed-phase and ion-interaction high performance liquid chromatography. Journal of Pharmaceutical and Biomedical Analysis 2005; 39: 438-443.
31. Riordain CO, Nesterenko P and Paull B. Zwitterionic ion chromatography with carboxybetaine surfactant-coated particle packed and monolithic type columns. Journal of Chromatography A 2005; 1070: 71-78.
32. Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A and Pappin DJ. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Molecular and Cellular Proteomics 2004; 3: 1154-1169.
33. Shen Y, Moore RJ, Zhao R, Blonder J, Auberry DL, Masselon C, Pasa-Tolic L, Hixson KK, Auberry KJ and Smith RD. High-efficiency on-line solid-phase extraction coupling to 15-150-micron-i.d. column liquid chromatography for proteomic analysis. Analytical Chemistry 2003; 75: 3596-3605.
34. Shen Y, Tolic N, Masselon C, Pasa-Tolic L, Camp DG, 2nd, Hixson KK, Zhao R, Anderson GA and Smith RD. Ultrasensitive proteomics using high-efficiency on-line micro-SPE-nanoLC-nanoESI MS and MS/MS. Analytical Chemistry 2004; 76: 144-154.
35. Smith AG, Heath JK, Donaldson DD, Wong GG, Moreau J, Stahl M and Rogers D. Inhibition of pluripotential embryonic stem cell differentiation by purified polypeptides. Nature 1988; 336: 688-690.
36. Strege MA, Stevenson S and Lawrence SM. Mixed-mode anion-cation exchange/ hydrophilic interaction liquid chromatography-electrospray mass spectrometry as an alternative to reversed phase for small molecule drug discovery. Analytical Chemistry 2000; 72: 4629-4633.
37. Takegawa Y, Deguchi K, Ito H, Keira T, Nakagawa H and Nishimura S. Simple separation of isomeric sialylated N-glycopeptides by a zwitterionic type of hydrophilic interaction chromatography. Journal of Separation Science 2006a; 29: 2533-2540.
38. Takegawa Y, Deguchi K, Keira T, Ito H, Nakagawa H and Nishimura S. Separation of isomeric 2-aminopyridine derivatized N-glycans and N-glycopeptides of human serum immunoglobulin G by using a zwitterionic type of hydrophilic-interaction chromatography. Journal of Chromatography A 2006b; 1113: 177-181.
39. Tolstikov VV and Fiehn O. Analysis of highly polar compounds of plant origin: combination of hydrophilic interaction chromatography and electrospray ion trap mass spectrometry. Analytical Biochemistry 2002; 301: 298-307.
40. Viklund C, Sjogren A, Irgum K and Nes I. Chromatographic interactions between proteins and sulfoalkylbetaine-based zwitterionic copolymers in fully aqueous low-salt buffers. Analytical Chemistry 2001; 73: 444-452.
41. Wa C, Cerny RL and Hage DS. Identification and quantitative studies of protein immobilization sites by stable isotope labeling and mass spectrometry. Analytical Chemistry 2006; 78: 7967-7977.
42. Wang H and Hanash S. Multi-dimensional liquid phase based separations in proteomics. Journal of Chromatography B, Analytical Technologies in the Biomedical and Life Sciences 2003; 787: 11-18.
43. Williams RL, Hilton DJ, Pease S, Willson TA, Stewart CL, Gearing DP, Wagner EF, Metcalf D, Nicola NA and Gough NM. Myeloid leukaemia inhibitory factor maintains the developmental potential of embryonic stem cells. Nature 1988; 336: 684-687.
44. Wu SL, Choudhary G, Ramstrom M, Bergquist J and Hancock WS. Evaluation of shotgun sequencing for proteomic analysis of human plasma using HPLC coupled with either ion trap or Fourier transform mass spectrometry. Journal of Proteome Research 2003; 2: 383-393.
45. Wu WW, Wang G, Baek SJ and Shen RF. Comparative study of three proteomic quantitative methods, DIGE, cICAT and iTRAQ, using 2D gel- or LC-MALDI TOF/TOF. Journal of Proteome Research 2006; 5: 651-658.
46. Xuan Y, Scheuermann EB, Meda AR, Hayen H, von Wiren N and Weber G. Separation and identification of phytosiderophores and their metal complexes in plants by zwitterionic hydrophilic interaction liquid chromatography coupled to electrospray ionization mass spectrometry. Journal of Chromatography A 2006; 1136: 73-81.
47. Zhang J and Wang DI. Quantitative analysis and process monitoring of site-specific glycosylation microheterogeneity in recombinant human interferon-gamma from Chinese hamster ovary cell culture by hydrophilic interaction chromatography. Journal of Chromatography B: Biomedical Sciences and Applications 1998; 712: 73-82.