Abstract
Mass spectrometry-based proteomics is the method of choice for analyzing (sub-) proteomes from virtually any source; with cells grown in culture being the most frequently investigated samples. Using HeLa cells, we describe a strategy for the optimization of protocols for whole proteome analysis. We cover cell lysis, protein precipitation and digestion, comparing the results obtained using different parameters and offering various possibilities for the optimization of a proteomic workflow which can be used for virtually any type of animal cell grown in culture.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Bogdanov B, Smith RD (2005) Proteomics by FTICR mass spectrometry: top down and bottom up. Mass Spectrom Rev 24:168–200
Winter D, Hung CW, Jaskolla TW et al (2012) Enzyme-cleavable tandem peptides for quantitative studies in MS-based proteomics. Proteomics 12:3470–3474
Winter D, Steen H (2011) Optimization of cell lysis and protein digestion protocols for the analysis of HeLa S3 cells by LC-MS/MS. Proteomics 11:4726–4730
Singh S, Winter D, Kirchner M et al (2014) Co-regulation proteomics reveals substrates and mechanisms of APC/C-dependent degradation. EMBO J 33:385–399
Villen J, Gygi SP (2008) The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry. Nat Protoc 3:1630–1638
Wisniewski JR, Zougman A, Nagaraj N et al (2009) Universal sample preparation method for proteome analysis. Nat Methods 6:359–362
Zahedi RP, Lewandrowski U, Wiesner J et al (2008) Phosphoproteome of resting human platelets. J Proteome Res 7:526–534
Sapan CV, Lundblad RL, Price NC (1999) Colorimetric protein assay techniques. Biotechnol Appl Biochem 29:99–108
Paulo JA, Lee LS, Wu B et al (2010) Optimized sample preparation of endoscopic collected pancreatic fluid for SDS-PAGE analysis. Electrophoresis 31:2377–2387
Jiang L, He L, Fountoulakis M (2004) Comparison of protein precipitation methods for sample preparation prior to proteomic analysis. J Chromatogr A 1023:317–320
Shevchenko A, Thomas H, Havlis J et al (2006) In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc 1:2856–2860
Yu YQ, Gilar M, Lee PJ et al (2003) Enzyme-friendly, mass spectrometry-compatible surfactant for in-solution enzymatic digestion of proteins. Anal Chem 75:6023–6028
Rappsilber J, Ishihama Y, Mann M (2003) Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal Chem 75:663–670
Bantscheff M, Schirle M, Sweetman G et al (2007) Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem 389:1017–1031
Acknowledgements
This work was supported by the German Academic Exchange Service (DAAD) and the 7th Framework Program of the European Union.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Winter, D., Dehghani, A., Steen, H. (2015). Optimization of Cell Lysis and Protein Digestion Protocols for Protein Analysis by LC-MS/MS. In: Posch, A. (eds) Proteomic Profiling. Methods in Molecular Biology, vol 1295. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2550-6_20
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2550-6_20
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2549-0
Online ISBN: 978-1-4939-2550-6
eBook Packages: Springer Protocols