New algorithm for 15N//14N quantitation with LC-ESI-MS using an LTQ-FT mass spectrometer

Victor P. Andreev, Lingyun Li, Tomas Rejtar, Qingbo Li, James G. Ferry, Barry L. Karger

Research output: Contribution to journalArticle

31 Citations (Scopus)

Abstract

A new algorithm (QN) for the 15N/14N quantitation of relative protein abundances in complex proteomic samples is described. QN takes advantage of the high resolution, mass accuracy and throughput of the hybrid mass spectrometer LTQ-FT MS. Peptide quantitation is based on MS peak intensity (measured in the FT MS), while peptide identification is performed in the MS/MS mode (measured in the LTQ linear ion trap). Accuracy of the protein abundance is enhanced by a novel scoring procedure, allowing filtering of less reliable measurements of peptide abundances. The performance of QN is illustrated in the relative quantitative analysis of M. acetivorans C2A cultures grown with carbon monoxide vs methanol as substrate. Roughly 1000 proteins were quantitated with an average CV of 9% for the protein abundance ratios. QN performs quantitation without manual intervention, does not require high processing power, and generates files compatible with the Guidelines for Proteomic Data Publication.

Original languageEnglish
Pages (from-to)2039-2045
Number of pages7
JournalJournal of Proteome Research
Volume5
Issue number8
DOIs
StatePublished - Aug 1 2006

Fingerprint

Mass spectrometers
Proteomics
Peptides
Proteins
Carbon Monoxide
Methanol
Publications
Throughput
Guidelines
Ions
Substrates
Processing
Chemical analysis

Keywords

  • LC-MS
  • M. acetivorans
  • Metabolic labeling
  • Quantitative proteomics
  • Software

ASJC Scopus subject areas

  • Genetics
  • Biotechnology
  • Biochemistry

Cite this

Andreev, V. P., Li, L., Rejtar, T., Li, Q., Ferry, J. G., & Karger, B. L. (2006). New algorithm for 15N//14N quantitation with LC-ESI-MS using an LTQ-FT mass spectrometer. Journal of Proteome Research, 5(8), 2039-2045. https://doi.org/10.1021/pr060105m

New algorithm for 15N//14N quantitation with LC-ESI-MS using an LTQ-FT mass spectrometer. / Andreev, Victor P.; Li, Lingyun; Rejtar, Tomas; Li, Qingbo; Ferry, James G.; Karger, Barry L.

In: Journal of Proteome Research, Vol. 5, No. 8, 01.08.2006, p. 2039-2045.

Research output: Contribution to journalArticle

Andreev, VP, Li, L, Rejtar, T, Li, Q, Ferry, JG & Karger, BL 2006, 'New algorithm for 15N//14N quantitation with LC-ESI-MS using an LTQ-FT mass spectrometer', Journal of Proteome Research, vol. 5, no. 8, pp. 2039-2045. https://doi.org/10.1021/pr060105m
Andreev, Victor P. ; Li, Lingyun ; Rejtar, Tomas ; Li, Qingbo ; Ferry, James G. ; Karger, Barry L. / New algorithm for 15N//14N quantitation with LC-ESI-MS using an LTQ-FT mass spectrometer. In: Journal of Proteome Research. 2006 ; Vol. 5, No. 8. pp. 2039-2045.
@article{534e17738c6743caa67210677515a5fc,
title = "New algorithm for 15N//14N quantitation with LC-ESI-MS using an LTQ-FT mass spectrometer",
abstract = "A new algorithm (QN) for the 15N/14N quantitation of relative protein abundances in complex proteomic samples is described. QN takes advantage of the high resolution, mass accuracy and throughput of the hybrid mass spectrometer LTQ-FT MS. Peptide quantitation is based on MS peak intensity (measured in the FT MS), while peptide identification is performed in the MS/MS mode (measured in the LTQ linear ion trap). Accuracy of the protein abundance is enhanced by a novel scoring procedure, allowing filtering of less reliable measurements of peptide abundances. The performance of QN is illustrated in the relative quantitative analysis of M. acetivorans C2A cultures grown with carbon monoxide vs methanol as substrate. Roughly 1000 proteins were quantitated with an average CV of 9{\%} for the protein abundance ratios. QN performs quantitation without manual intervention, does not require high processing power, and generates files compatible with the Guidelines for Proteomic Data Publication.",
keywords = "LC-MS, M. acetivorans, Metabolic labeling, Quantitative proteomics, Software",
author = "Andreev, {Victor P.} and Lingyun Li and Tomas Rejtar and Qingbo Li and Ferry, {James G.} and Karger, {Barry L.}",
year = "2006",
month = "8",
day = "1",
doi = "10.1021/pr060105m",
language = "English",
volume = "5",
pages = "2039--2045",
journal = "Journal of Proteome Research",
issn = "1535-3893",
publisher = "American Chemical Society",
number = "8",

}

TY - JOUR

T1 - New algorithm for 15N//14N quantitation with LC-ESI-MS using an LTQ-FT mass spectrometer

AU - Andreev, Victor P.

AU - Li, Lingyun

AU - Rejtar, Tomas

AU - Li, Qingbo

AU - Ferry, James G.

AU - Karger, Barry L.

PY - 2006/8/1

Y1 - 2006/8/1

N2 - A new algorithm (QN) for the 15N/14N quantitation of relative protein abundances in complex proteomic samples is described. QN takes advantage of the high resolution, mass accuracy and throughput of the hybrid mass spectrometer LTQ-FT MS. Peptide quantitation is based on MS peak intensity (measured in the FT MS), while peptide identification is performed in the MS/MS mode (measured in the LTQ linear ion trap). Accuracy of the protein abundance is enhanced by a novel scoring procedure, allowing filtering of less reliable measurements of peptide abundances. The performance of QN is illustrated in the relative quantitative analysis of M. acetivorans C2A cultures grown with carbon monoxide vs methanol as substrate. Roughly 1000 proteins were quantitated with an average CV of 9% for the protein abundance ratios. QN performs quantitation without manual intervention, does not require high processing power, and generates files compatible with the Guidelines for Proteomic Data Publication.

AB - A new algorithm (QN) for the 15N/14N quantitation of relative protein abundances in complex proteomic samples is described. QN takes advantage of the high resolution, mass accuracy and throughput of the hybrid mass spectrometer LTQ-FT MS. Peptide quantitation is based on MS peak intensity (measured in the FT MS), while peptide identification is performed in the MS/MS mode (measured in the LTQ linear ion trap). Accuracy of the protein abundance is enhanced by a novel scoring procedure, allowing filtering of less reliable measurements of peptide abundances. The performance of QN is illustrated in the relative quantitative analysis of M. acetivorans C2A cultures grown with carbon monoxide vs methanol as substrate. Roughly 1000 proteins were quantitated with an average CV of 9% for the protein abundance ratios. QN performs quantitation without manual intervention, does not require high processing power, and generates files compatible with the Guidelines for Proteomic Data Publication.

KW - LC-MS

KW - M. acetivorans

KW - Metabolic labeling

KW - Quantitative proteomics

KW - Software

UR - http://www.scopus.com/inward/record.url?scp=33747197432&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33747197432&partnerID=8YFLogxK

U2 - 10.1021/pr060105m

DO - 10.1021/pr060105m

M3 - Article

C2 - 16889428

AN - SCOPUS:33747197432

VL - 5

SP - 2039

EP - 2045

JO - Journal of Proteome Research

JF - Journal of Proteome Research

SN - 1535-3893

IS - 8

ER -