Technical Brief

LTQ-iQuant: A freely available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from LTQ instruments

  1. Getiria Onsongo1,
  2. Matthew D. Stone2,
  3. Susan K. Van Riper3,
  4. John Chilton4,
  5. Baolin Wu5,
  6. LeeAnn Higgins2,
  7. Troy C. Lund6,
  8. John V. Carlis1,
  9. Timothy J. Griffin2,*

Article first published online: 7 SEP 2010

DOI: 10.1002/pmic.201000189

Issue

PROTEOMICS

PROTEOMICS

Volume 10, Issue 19, pages 3533–3538, October 2010

Additional Information

How to Cite

Onsongo, G., Stone, M. D., Van Riper, S. K., Chilton, J., Wu, B., Higgins, L., Lund, T. C., Carlis, J. V. and Griffin, T. J. (2010), LTQ-iQuant: A freely available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from LTQ instruments. Proteomics, 10: 3533–3538. doi: 10.1002/pmic.201000189

Author Information

  1. 1

    Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA

  2. 2

    Departments of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA

  3. 3

    Departments of Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, MN, USA

  4. 4

    Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA

  5. 5

    Department of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA

  6. 6

    Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA

*Departments of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church St SE, 6-155 Jackson Hall, Minneapolis, MN 55455, USA Fax: +1-612-624-0432

Publication History

  1. Issue published online: 2 AUG 2010
  2. Article first published online: 7 SEP 2010
  3. Accepted manuscript online: 2 AUG 2010 12:00AM EST
  4. Manuscript Accepted: 16 JUL 2010
  5. Manuscript Revised: 29 JUN 2010
  6. Manuscript Received: 22 MAR 2010

Funded by

  • NIH grant. Grant Number: 1R01DE017734

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Keywords:

  • Bioinformatics;
  • Isobaric tags;
  • LTQ;
  • Protein quantification;
  • Open source software;
  • Weighted average

Abstract

Pulsed Q dissociation enables combining LTQ ion trap instruments with isobaric peptide tagging. Unfortunately, this combination lacks a technique which accurately reports protein abundance ratios and is implemented in a freely available, flexible software pipeline. We developed and implemented a technique assigning collective reporter ion intensity-based weights to each peptide abundance ratio and calculating a protein's weighted average abundance ratio and p-value. Using an iTRAQ-labeled standard mixture, we compared our technique's performance to the commercial software MASCOT, finding that it performed better than MASCOT's nonweighted averaging and median peptide ratio techniques, and equal to its weighted averaging technique. We also compared performance of the LTQ-Orbitrap plus our technique to 4800 MALDI TOF/TOF plus Protein Pilot, by analyzing an iTRAQ-labeled stem cell lysate. We found highly correlated protein abundance ratios, indicating that the LTQ-Orbitrap plus our technique yields results comparable to the current standard. We implemented our technique in a freely available, automated software pipeline, called LTQ-iQuant, which is mzXML-compatible; supports iTRAQ 4-plex and 8-plex LTQ data; and can be modified for and have weights trained to a user's LTQ and other isobaric peptide tagging methods. LTQ-iQuant should make LTQ instruments and isobaric peptide tagging accessible to more proteomic researchers.

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