Characterization of a digested protein complex with quantitative aspects: an approach based on accurate mass chromatographic analysis with Fourier transform-ion cyclotron resonance mass spectrometry

Proteomics
Takemichi NakamuraKoji Takio

Abstract

We describe a new approach for the characterization of a digested protein complex with quantitative aspects. Accurate masses of tryptic peptides in the digested complex were acquired by nano-liquid chromatography Fourier transform-ion cyclotron resonance mass spectrometry (MS). The conditions of the electrospray ion source were alternated to acquire normal and fragment-ion-rich mass spectra concurrently. This, alternating-scan method, which includes no tandem mass spectrometry (MS/MS), allowed us to retain the integrity of the mass chromatograms and averted missed peptides due to MS and MS/MS switching. Tentative assignments of accurate peptide masses were verified with the concurrently acquired fragment-ion-rich spectra, and the identities of the protein components were established. For each identified protein component, mass chromatograms attributable to the validated accurate peptide masses were extracted, and the peak areas of multiple mass chromatograms were standardized. The standardized peak areas appeared to reasonably reflect the molar ratio of the protein components in standard mixtures. This new approach was successfully applied to the characterization of a cyanobacterial photosystem II complex preparation. A clear d...Continue Reading

Citations

Aug 2, 2007·Analytical and Bioanalytical Chemistry·Marcus BantscheffBernhard Kuster
Jun 28, 2005·Journal of the American Society for Mass Spectrometry·Angela D NorbeckRichard D Smith
May 9, 2008·The Journal of Biological Chemistry·Tatsuro ShimamuraMasashi Miyano
Dec 13, 2006·Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences·Catherine Fenselau
Mar 8, 2005·Journal of Mass Spectrometry : JMS
Aug 1, 2012·Mass Spectrometry Reviews·Eva Rodríguez-Suárez, Anthony D Whetton
Jul 15, 2009·Mass Spectrometry Reviews·Xinyu LiuYu-Quan Wei
Nov 22, 2017·Science Advances·Daniel A WeiszHimadri B Pakrasi
Jun 15, 2007·Laboratory Investigation; a Journal of Technical Methods and Pathology·Rajagopalan SudhaMichael B Prystowsky

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