Mass Spectrometric Analysis of Proteins

  • Rod Chalk
Part of the Methods in Molecular Biology book series (MIMB, volume 1586)


Mass spectrometry is a generic technique for the structural and functional analysis of purified proteins. Instrument capabilities and the possibilities of intact protein, peptide fragmentation and native analyses are discussed. Detailed experimental protocols are described for the most commonly applied techniques of protein identification, posttranslational modification (PTM) characterization, PTM mapping, native mass spectrometry, and analysis of membrane proteins using electrospray mass spectrometry.

Key words

Mass spectrometry Electrospray Liquid chromatography–mass spectrometry LC-MS Tandem mass spectrometry LC-MSMS Protein Posttranslational modification PTM Native mass spectrometry Integral membrane proteins IMPs SDS-PAGE Size exclusion chromatography SEC High pressure liquid chromatography HPLC Phosphorylation Glycan 



The SGC is a registered charity (number 1097737) that receives funds from AbbVie, Bayer Pharma AG, Boehringer Ingelheim, Canada Foundation for Innovation, Eshelman Institute for Innovation, Genome Canada, Innovative Medicines Initiative (EU/EFPIA) [ULTRA-DD grant no. 115766], Janssen, Merck & Co., Novartis Pharma AG, Ontario Ministry of Economic Development and Innovation, Pfizer, São Paulo Research Foundation-FAPESP, Takeda, and Wellcome Trust [092809/Z/10/Z].


  1. 1.
    Karas M, Bachmann D, Hillenkamp F (1985) Influence of the wavelength in high-irradiance ultraviolet-laser desorption mass-spectrometry of organic-molecules. Anal Chem 57:2935–2939CrossRefGoogle Scholar
  2. 2.
    Dole M, Mack LL, Hines RL et al (1968) Molecular beams of macroions. J Chem Phys 49:2240–2249CrossRefGoogle Scholar
  3. 3.
    Lewis JK, Wei J, Siuzdak G (2006) Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry in Peptide and Protein Analysis. Encyclopedia of Analytical Chemistry. Published Online: 15 SEP 2006 DOI:  10.1002/9780470027318.a1621
  4. 4.
    Anderson NL, Anderson NG (1998) Proteome and proteomics: new technologies, new concepts, and new words. Electrophoresis 19:1853–1861CrossRefPubMedGoogle Scholar
  5. 5.
    Cole RB (2011) Electrospray and MALDI mass spectrometry: fundamentals, instrumentation, practicalities, and biological applications. John Wiley & Sons, Hoboken, NJGoogle Scholar
  6. 6.
    Garcia BA, Mollah S, Ueberheide BM et al (2007) Chemical derivatization of histones for facilitated analysis by mass spectrometry. Nat Protoc 2:933–938CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Ong S-E, Blagoev B, Kratchmarova I et al (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1:376–386CrossRefPubMedGoogle Scholar
  8. 8.
    Thingholm TE, Jørgensen TJ, Jensen ON et al (2006) Highly selective enrichment of phosphorylated peptides using titanium dioxide. Nat Protoc 1:1929–1935CrossRefPubMedGoogle Scholar
  9. 9.
    Rye PT, Frick LE, Ozbal CC et al (2011) Advances in label-free screening approaches for studying sirtuin-mediated deacetylation. J Biomol Screen 16:1217–1226CrossRefPubMedGoogle Scholar
  10. 10.
    Berridge G, Chalk R, D’Avanzo N et al (2011) High-performance liquid chromatography separation and intact mass analysis of detergent-solubilized integral membrane proteins. Anal Biochem 410:272–280CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Chalk R, Berridge G, Shrestha L et al (2014) High-throughput mass spectrometry applied to structural genomics. Chromatography 1:159–175CrossRefGoogle Scholar
  12. 12.
    Khoshnoodi J, Hill S, Tryggvason K et al (2007) Identification of N-linked glycosylation sites in human nephrin using mass spectrometry. J Mass Spectrom 42:370–379CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Structural Genomics Consortium (SGC), Nuffield Department of MedicineUniversity of OxfordOxfordUK

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