Molecular-level description of proteins from Saccharomyces cerevisiae using quadrupole FT hybrid mass spectrometry for top down proteomics

Fanyu Meng, Yi Du, Leah M. Miller, Steven M. Patrie, Dana E. Robinson, Neil L. Kelleher

Research output: Contribution to journalArticle

60 Citations (Scopus)

Abstract

For improved detection of diverse posttranslational modifications (PTMs), direct fragmentation of protein ions by top down mass spectrometry holds promise but has yet to be achieved on a large scale. Using lysate from Saccharomyces cerevisiae, 117 gene products were identified with 100% sequence coverage revealing 26 acetylations, 1 N-terminal dimethylation, 1 phosphorylation, 18 duplicate genes, and 44 proteolytic fragments. The platform for this study combined continuous-elution gel electrophoresis, reversed-phase liquid chromatography, automated nanospray coupled with a quadrupole-FT hybrid mass spectrometer, and a new search engine for querying a custom database. The proteins identified required no manual validation, ranged from 5 to 39 kDa, had codon biases from 0.93 to 0.083, and were primarily associated with glycolysis and protein synthesis. Illustrations of gene-specific identifications, PTM detection and subsequent PTM localization (using either electron capture dissociation or known PTM data stored in a database) show how larger scale proteome projects incorporating top down may proceed in the future using commercial Q-FT instruments.

Original languageEnglish (US)
Pages (from-to)2852-2858
Number of pages7
JournalAnalytical Chemistry
Volume76
Issue number10
DOIs
StatePublished - May 15 2004

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Saccharomyces cerevisiae Proteins
Mass spectrometry
Genes
Acetylation
Phosphorylation
Proteins
Liquid chromatography
Mass spectrometers
Proteome
Search engines
Electrophoresis
Yeast
Gels
Ions
Electrons
Proteomics

ASJC Scopus subject areas

  • Analytical Chemistry

Cite this

Molecular-level description of proteins from Saccharomyces cerevisiae using quadrupole FT hybrid mass spectrometry for top down proteomics. / Meng, Fanyu; Du, Yi; Miller, Leah M.; Patrie, Steven M.; Robinson, Dana E.; Kelleher, Neil L.

In: Analytical Chemistry, Vol. 76, No. 10, 15.05.2004, p. 2852-2858.

Research output: Contribution to journalArticle

Meng, Fanyu ; Du, Yi ; Miller, Leah M. ; Patrie, Steven M. ; Robinson, Dana E. ; Kelleher, Neil L. / Molecular-level description of proteins from Saccharomyces cerevisiae using quadrupole FT hybrid mass spectrometry for top down proteomics. In: Analytical Chemistry. 2004 ; Vol. 76, No. 10. pp. 2852-2858.
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