IPG strip-based peptide fractionation for shotgun proteomics

Methods in Molecular Biology

Volumn 1156, Issue , 2014, Pages 67-77

  Eravci, Murat ^a   Sommer, Christian ^a   Selbach, Matthias ^a  

^a NONE

Author keywords

Immobilized pH gradient (IPG); Isoelectric focusing (IEF); Peptide fractionation; Shotgun proteomics

Indexed keywords

PEPTIDE;

ANALYTICAL EQUIPMENT; ARTICLE; IMMOBILIZED PH GRADIENT GEL STRIP; ISOELECTRIC FOCUSING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PEPTIDE FRACTIONATION; PH; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; REPRODUCIBILITY; HEK293 CELL LINE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; ISOLATION AND PURIFICATION; REVERSED PHASE LIQUID CHROMATOGRAPHY;

CHROMATOGRAPHY, HIGH PRESSURE LIQUID; CHROMATOGRAPHY, REVERSE-PHASE; HEK293 CELLS; HUMANS; HYDROGEN-ION CONCENTRATION; ISOELECTRIC FOCUSING; PEPTIDES; PROTEOMICS;

EID: 84922395302     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-0685-7_5     Document Type: Article

References (16)

1. Lahm HW, Langen H (2000) Mass spectrometry: a tool for the identifi cation of proteins separated by gels. Electrophoesis 21:2105–2114
2. Ishihama Y, Rappsilber J, Mann M (2006) Modular stop and go extraction tips with stacked disks for parallel and multidimensional peptide fractionation in proteomics. J Proteome Res 5:988–994
3. Cargile BJ, Bundy JL, Freeman TW, Stephenson JL Jr (2004) Gel based isoelectricfocusing of peptides and the utility of isoelectric point in protein identifi cation. J Proteome Res 3:112–119
4. Krijgsveld J, Gauci S, Dormeyer W, Heck AJJ (2006) In-gel isoelectric focusing of peptides as a tool for improved protein identifi cation. J Proteome Res 5:1721–1730
5. Slebos RJ, Brock JW, Winters NF, Stuart SR, Martinez MA, Li M, Chambers MC, Zimmerman LJ, Ham AJ, Tabb DL, Liebler DC (2008) Evaluation of strong cation exchange versus isoelectric focusing of peptides for multidimensional liquid chromatographytandem mass spectrometry. J Proteome Res 7:5286–5294
6. Cargile BJ, Talley DL, Stephenson JL Jr (2004) Immobilized pH gradients as a fi rst dimension in shotgun proteomics and analysis of the accuracy of pI predictability of peptides. Electrophoresis 25:936–945
7. Xie H, Bandhakavi S, Roe MR, Griffi n TJ (2008) Preparative peptide isoelectric focusing as a tool for improving the identifi cation of lysine-acetylated peptides from complex mixtures. J Proteome Res 5:2019–2026
8. Hörth P, Miller CA, Preckel T, Wenz C (2006) Effi cient fractionation and improved protein identifi cation by peptide OFFGEL electrophoresis. Mol Cell Proteomics 10:1968–1974
9. Hubner NC, Ren S, Mann M (2008) Peptide separation with immobilized pI strips is an attractive alternative to in-gel protein digestion for proteome analysis. Proteomics 8:4862–4872
10. Sanchez JC, Rouge V, Pisteur M, Ravier F, Tonella L, Moosmayer M, Wilkins MR, Hochstrasser D (1997) Improved and simplifi ed in-gel sample application using reswelling of dry immobilized pH gradients. Electrophoresis 18:324–327
11. Wessel D, Fluegge UI (1984) A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal Biochem 138:141–143
12. Rappsilber J, Mann M, Ishihama Y (2007) Protocol for micro-purifi cation, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc 2:1896–1906
13. Kelstrup CD, Young C, Lavallee R, Nielsen ML, Olsen JV (2012) Optimized fast and sensitive acquisition methods for shotgun proteomics on a quadrupole orbitrap mass spectrometer. J Proteome Res 11:3487–3497
14. Eravci M, Fuxius S, Broedel O, Weist S, Eravci S, Mansmann U, Schluter H, Tiemann J, Baumgartner A (2007) Improved comparative proteome analysis based on two-dimensional gel electrophoresis. Proteomics 7:513–523
15. Viswanatha T, Liener IE (1955) The inhibition of trypsin: III. Infl uence of urea. J Biol Chem 215:777–785
16. Vaezzadeh AR, Hernandez C, Vadas O, Deshusses JJ, Lescuyer P, Lisacek F, Hochstrasser DF (2008) PICarver: a software tool and strategy for peptides isoelectric focusing. J Proteome Res 7:4336–4345