Combining isoelectric point-based fractionation, liquid chromatography and mass spectrometry to improve peptide detection and protein identification

Journal of the American Society for Mass Spectrometry

Volumn 21, Issue 9, 2010, Pages 1612-1619

  Cologna, Stephanie M ^a   Russell, William K ^a   Lim, Peniel J ^a   Vigh, Gyula ^a   Russell, David H ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTES; COMPLEX MIXTURE; DYNAMIC RANGE; HIGH CAPACITY; HIGH-THROUGHPUT; ION SUPPRESSION; ISO-ELECTRIC POINTS; ISOELECTRIC; ISOELECTRIC FOCUSING; ISOELECTRIC POINT (PI); PEPTIDE DETECTION; PEPTIDE IONS; PH RANGE; PH VALUE; PREFRACTIONATION; PROTEIN IDENTIFICATION; PROTEOMIC STUDIES; SAMPLE CLEAN-UP; SEPARATED WELLS; SMALL SAMPLES; TRAPPING DEVICES; TRYPTIC PEPTIDES;

ELECTROPHORESIS; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MEMBRANES; PH EFFECTS;

PEPTIDES;

ION; PEPTIDE; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; CONTROLLED STUDY; HIGH THROUGHPUT SCREENING; ION TRAP MASS SPECTROMETRY; ISOELECTRIC FOCUSING; ISOELECTRIC POINT; LIQUID CHROMATOGRAPHY; MEMBRANE SEPARATED WELLS FOR ISOELECTRIC FOCUSING AND TRAPPING; MOLECULAR DYNAMICS; NONHUMAN; PEPTIDE ANALYSIS; PROTEIN ANALYSIS; PROTEIN DEGRADATION;

ANIMALS; CHEMICAL FRACTIONATION; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; COMPLEX MIXTURES; FUNGAL PROTEINS; HIGH-THROUGHPUT SCREENING ASSAYS; ISOELECTRIC FOCUSING; ISOELECTRIC POINT; MEMBRANES, ARTIFICIAL; PEPTIDE MAPPING; PROTEINS; PROTEOMICS; SACCHAROMYCES CEREVISIAE; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 77955918300     PISSN: 10440305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jasms.2010.04.010     Document Type: Article

References (46)

1. Righetti P.G., Castagna A., Herbert B., Reymond F., Rossier J.S. Prefractionation Techniques in Proteome Analysis. Proteomics 2003, 3:1397-1407.
2. Kolin A. Separation and Concentration of Proteins in a pH Field Combined with an Electric Field. J. Chem. Phys. 1954, 22:1628-1629.
3. Svensson H. Isoelectric Fractionation, Analysis, and Characterization of Ampholytes in Natural pH Gradients. 1. Differential Equation of Solute Concentrations at a Steady State and Its Solution for Simple Cases. Acta Chem. Scand. 1961, 15:325-341.
4. Gygi S.P., Corthals G.L., Zhang Y., Rochon Y., Aebersold R. Evaluation of Two-Dimensional Gel Electrophoresis-Based Proteome Analysis Technology. Proc. Natl. Acad. Sci. U.S.A. 2000, 97:9390-9395.
5. Jensen P.K., Pasa-Tolic L., Anderson G.A., Horner J.A., Lipton M.S., Bruce J.E., Smith R.D. Probing Proteomes Using Capillary Isoelectric Focusing-Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Anal. Chem. 1999, 71:2076-2084.
6. Heller M., Michel P., Morier P., Crettaz D., Wenz C., Tissot J.D., Reymond F., Rossier J.S. Two Stage Off-Gel Isoelectric Focusing: Protein Followed by Peptide Fractionation and Application to Proteome Analysis of Human Plasma. Electrophoresis 2005, 26:1174-1188.
7. Righetti P.G., Bossi A., Wenisch E., Orsini G. Protein Purification in Multicompartment Electrolyzers with Isoelectric Membranes. J. Chromatogr. B 1997, 699:105-115.
8. Righetti P.G., Bossi A. Isoelectric Focusing of Proteins and Peptides in Gel Slabs and in Capillaries. Anal. Chim. Acta 1998, 372:1-19.
9. Anderson L., Anderson N.G. High-Resolution 2-Dimensional Electrophoresis of Human-Plasma Proteins. Proc. Natl. Acad. Sci. U.S.A. 1977, 74:5421-5425.
10. Anderson N.L., Anderson N.G. A Two-Dimensional Gel Database of Human Plasma-Proteins. Electrophoresis 1991, 12:883-906.
11. Henzel W.J., Billeci T.M., Stults J.T., Wong S.C., Grimley C., Watanabe C. Identifying Proteins from Two-Dimensional Gels by Molecular Mass Searching of Peptide-Fragments in Protein-Sequence Databases. Proc. Natl. Acad. Sci. U.S.A. 1993, 90:5011-5015.
12. Gorg A., Weiss W., Dunn M.J. Current Two-Dimensional Electrophoresis Technology for Proteomics. Proteomics 2004, 4:3665-3685.
13. Righetti P.G., Barzaghi B., Luzzana M., Manfredi G., Faupel M. A Horizontal Apparatus for Isoelectric Protein-Purification in a Segmented Immobilized pH Gradient. J. Biochem. Biophys. Methods 1987, 15:189-198.
14. Zuo X., Speicher D.W. A Method for Global Analysis of Complex Proteomes Using Sample Prefractionation by Solution Isoelectrofocusing Prior to Two-Dimensional Electrophoresis. Anal. Biochem. 2000, 284:266-278.
15. Ros A., Faupel M., Mees H., van Oostrum J., Ferrigno R., Reymond F., Michel P., Rossier J.S., Girault H.H. Protein Purification by Off-Gel Electrophoresis. Proteomics 2002, 2:151-156.
16. Ramachandran P., Boontheung P., Xie Y.M., Sondej M., Wong D.T., Loo J.A. Identification of N-Linked Glycoproteins in Human Saliva by Glycoprotein Capture and Mass Spectrometry. J. Proteome Res. 2006, 5:1493-1503.
17. Han M.J., Herlyn M., Fisher A.B., Speicher D.W. Microscale Solution Ief Combined with 2-D Dige Substantially Enhances Analysis Depth of Complex Proteomes Such As Mammalian Cell and Tissue Extracts. Electrophoresis 2008, 29:695-705.
18. Myung J.-K., Lubec G. Use of Solution-Ief-Fractionation Leads to Separation of 2673 Mouse Brain Proteins Including 255 Hydrophobic Structures. J. Proteome Res. 2008, 5:1267-1275.
19. Michel P.E., Crettaz D., Morier P., Heller M., Gallot D., Tissot J.D., Reymond F., Rossier J.S. Proteome Analysis of Human Plasma and Amniotic Fluid by Off-Gel (Tm) Isoelectric Focusing Followed by Nano-LC-MS/MS. Electrophoresis 2006, 27:1169-1181.
20. Herbert B., Righetti P.G. A Turning Point in Proteome Analysis: Sample Prefractionation Via Multicompartment Electrolyzers with Isoelectric Membranes. Electrophoresis 2000, 21:3639-3648.
21. Martin A.J.P., Hampson F. New Apparatus for Isoelectric-Focusing. J. Chromatogr. 1978, 159:101-110.
22. Ogle D., Ho A., Gibson T., Rylatt D., Shave E., Lim P., Vigh G. Preparative-Scale Isoelectric Trapping Separations Using a Modified Gradiflow Unit. J. Chromatogr. A 2002, 979:155-161.
23. EsteveRomero J.S., Bossi A., Righetti P.G. Purification of Thermamylase in Multicompartment Electrolyzers with Isoelectric Membranes: The Problem of Protein Solubility. Electrophoresis 1996, 17:1242-1247.
24. Shave E., Vigh G. Preparative-Scale, Recirculating, pH-Biased Binary Isoelectric Trapping Separations. Electrophoresis 2004, 25:381-387.
25. Lim P., North R., Vigh G. Rapid Isoelectric Trapping in a Micropreparative-Scale Multicompartment Electrolyzer. Electrophoresis 2007, 28:1851-1859.
26. Waller L.N., Shores K., Knapp D.R. Shotgun Proteomic Analysis of Cerebrospinal Fluid Using Off-Gel Electrophoresis as the First-Dimension Separation. J. Proteome Res. 2008, 7:4577-4584.
27. Manadas B., English J.A., Wynne K.J., Cotter D.R., Dunn M.J. Comparative Analysis of Off-Gel, Strong Cation Exchange with pH Gradient, and Rp at High pH for First-Dimensional Separation of Peptides from a Membrane-Enriched Protein Fraction. Proteomics 2009, 9:5194-5198.
28. Hubner N.C., Ren S., Mann M. Peptide Separation with Immobilized Pi Strips Is an Attractive Alternative to in-Gel Protein Digestion for Proteome Analysis. Proteomics 2008, 8:4862-4872.
29. de Godoy L.M.F., Olsen J.V., Cox J., Nielsen M.L., Hubner N.C., Frohlich F., Walther T.C., Mann M. Comprehensive Mass-Spectrometry-Based Proteome Quantification of Haploid Versus Diploid Yeast. Nature 2008, 455:1251-1260.
30. Lengqvist J., Uhlen K., Lehtio J. iTRAQ Compatibility of Peptide Immobilized pH Gradient Isoelectric Focusing. Proteomics 2007, 7:1746-1752.
31. Chenau J., Michelland S., Sidibe J., Seve M. Peptides Off-Gel Electrophoresis: A Suitable Preanalytical Step for Complex Eukaryotic Samples Fractionation Compatible with Quantitative iTRAQ Labeling. Proteome Sci. 2008, 6:9.
32. Lim P. Dissertation 2006, Texas A and M University, College Station.
33. Lalwani S., Shave E., Vigh G. High-Buffering Capacity Hydrolytically Stable, Low-Pl Isoelectric Membranes for Isoelectric Trapping Separations. Electrophoresis 2004, 25:3323-3330.
34. Lalwani S., Shave E., Fleisher H.C., Nzeadibe K., Busby M.B., Vigh G. Alkali-Stable High-Pl Isoelectric Membranes for Isoelectric Trapping Separations. Electrophoresis 2004, 25:2128-2138.
35. Fleisher H.C., Vigh G. Hydrolytically Stable, Diaminocarboxylic Acid-Based Membranes Buffering in the pH Range from 6 to 8.5 for Isoelectric Trapping Separations. Electrophoresis 2005, 26:2511-2519.
36. Fleisher-Craver H.C., Vigh G. PVA-Based Tunable Buffering Membranes for Isoelectric Trapping Separations. Electrophoresis 2008, 29:4247-4256.
37. Gasteiger E., Gattiker A., Hoogland C., Ivanyi I., Appel R.D., Bairoch A. ExPASy: The Proteomics Server for In-Depth Protein Knowledge and Analysis. Nucleic Acids Res. 2003, 31:3784-3788.
38. Bradford M.M. Rapid and Sensitive Method for Quantitation of Microgram Quantities of Protein Utilizing Principle of Protein-Dye Binding. Anal. Biochem. 1976, 72:248-254.
39. Rosas-Acosta G., Russell W.K., Deyrieux A., Russell D.H., Wilson V.G. A Universal Strategy for Proteomic Studies of Sumo and Other Ubiquitin-Like Modifiers. Mol. Cell. Proteom. 2005, 4:56-72.
40. Perkins D.N., Pappin D.J.C., Creasy D.M., Cottrell J.S. Probability-Based Protein Identification by Searching Sequence Databases Using Mass Spectrometry Data. Electrophoresis 1999, 20:3551-3567.
41. Knochenmuss R., Stortelder A., Breuker K., Zenobi R. Secondary Ion-Molecule Reactions in Matrix-Assisted Laser Desorption/Ionization. J. Mass Spectrom. 2000, 35:1237-1245.
42. Cargile B.J., Stephenson J.L. An Alternative to Tandem Mass Spectrometry: Isoelectric Point and Accurate Mass for the Identification of Peptides. Anal. Chem. 2004, 76:267-275.
43. Washburn M.P., Wolters D., Yates J.R. Large-Scale Analysis of the Yeast Proteome by Multidimensional Protein Identification Technology. Nat. Biotechnol. 2001, 19:242-247.
44. Breci L., Hattrup E., Keeler M., Letarte J., Johnson R., Haynes P.A. Comprehensive Proteomics in Yeast Using Chromatographic Fractionation, Gas Phase Fractionation, Protein Gel Electrophoresis, and Isoelectric Focusing. Proteomics 2005, 5:2018-2028.
45. Cargile B.J., Talley D.L., Stephenson J.L. Immobilized pH Gradients as a First Dimension in Shotgun Proteomics and Analysis of the Accuracy of Pi Predictability of Peptides. Electrophoresis 2004, 25:936-945.
46. Cargile B.J., Sevinsky J.R., Essader A.S., Stephenson J.L., Bundy J.L. Immobilized pH Gradient Isoelectric Focusing as a First-Dimension Separation in Shotgun Proteomics. J. Biomol. Techniques 2005, 16:181-189.