Strategies for automating top-down protein analysis with Q-FTICR MS

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

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

Thirty years after its invention, the Fourier transform ion cyclotron resonance (FTICR) mass spectrometer continues its evolution into an enabling technology to deepen our understanding of biological systems. For contemporary protein analysis, a quadrupole FTICR hybrid with electrospray ionization is forwarded here as an engine for high resolution tandem mass spectrometry in a high-throughput setting. Three basic strategies for MS/MS of ions >10 kDa are illustrated by identification and characterization of proteins from stationary-phase yeast cells. From samples containing 1-13 proteins, introduced by a nanospray robot, 2-6 can be isolated automatically and fragmented in 15-45 min. Features used commonly for peptide analyses (e.g., multidimensional separations, data dependent acquisition, and probability-based protein identification) are now available in an off-line top-down platform. In one set of 9 samples, 20 proteins (6-17 kDa) were processed through the platform yielding a mean Pscore=0.002 (99.8% identification confidence) upon database retrieval with characterization of N-terminal post-translational modifications. On occasion of his 60th birthday, we offer this work in celebration of the steadily advancing technology that Alan Marshall helped to invent (now in over 400+ labs worldwide).

Original languageEnglish (US)
Pages (from-to)175-184
Number of pages10
JournalInternational Journal of Mass Spectrometry
Volume234
Issue number1-3
DOIs
StatePublished - May 1 2004

Fingerprint

Cyclotron resonance
cyclotron resonance
Fourier transforms
Ions
proteins
Proteins
ions
platforms
Electrospray ionization
inventions
yeast
Patents and inventions
Mass spectrometers
Biological systems
robots
Yeast
Peptides
mass spectrometers
peptides
retrieval

Keywords

  • FTICR
  • FTMS
  • Proteomics
  • Top-down

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Spectroscopy

Cite this

Strategies for automating top-down protein analysis with Q-FTICR MS. / Patrie, Steven M.; Robinson, Dana E.; Meng, Fanyu; Du, Yi; Kelleher, Neil L.

In: International Journal of Mass Spectrometry, Vol. 234, No. 1-3, 01.05.2004, p. 175-184.

Research output: Contribution to journalArticle

Patrie, Steven M. ; Robinson, Dana E. ; Meng, Fanyu ; Du, Yi ; Kelleher, Neil L. / Strategies for automating top-down protein analysis with Q-FTICR MS. In: International Journal of Mass Spectrometry. 2004 ; Vol. 234, No. 1-3. pp. 175-184.
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