Processing complex mixtures of intact proteins for direct analysis by mass spectrometry

Fanyu Meng, Benjamin J. Cargile, Steven M. Patrie, Jeffrey R. Johnson, Shaun M. McLoughlin, Neil L. Kelleher*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

160 Scopus citations


For analysis of intact proteins by mass spectrometry (MS), a new twist to a two-dimensional approach to proteome fractionation employs an acid-labile detergent instead of sodium dodecyl sulfate during continuous-elution gel electrophoresis. Use of this acid-labile surfactant (ALS) facilitates subsequent reversed-phase liquid chromatography (RPLC) for a net two-dimensional fractionation illustrated by transforming thousands of intact proteins from Saccharomyces cerevisiae to mixtures of 5-20 components (all within ∼5 kDa of one another) for presentation via electrospray ionization (ESI) to a Fourier transform MS (FTMS). Between 3 and 13 proteins have been detected directly using ESI-FTMS (or MALDI-TOF), and the fractionation showed a peak capacity of ∼400 between 0 and 70 kDa. A probability-based identification was made automatically from raw MS/MS data (obtained using a quadrupole-FTMS hybrid instrument) for one protein that differed from that predicted in a yeast database of ∼19 000 protein forms. This ALS-PAGE/RPLC approach to proteome processing ameliorates the "front end" problem that accompanies direct analysis of whole proteins and assists the future realization of protein identification with 100% sequence coverage in a high-throughput format.

Original languageEnglish (US)
Pages (from-to)2923-2929
Number of pages7
JournalAnalytical Chemistry
Issue number13
StatePublished - Jul 1 2002

ASJC Scopus subject areas

  • Analytical Chemistry


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