LTQ-iQuant: A freely available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from LTQ instruments
In: PROTEOMICS, Jg. 10 (2010-09-07), S. 3533-3538
Online
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Zugriff:
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 non-weighted 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 proteomics researchers.
Titel: |
LTQ-iQuant: A freely available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from LTQ instruments
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Autor/in / Beteiligte Person: | Lund, Troy C. ; Wu, Baolin ; Higgins, LeeAnn ; Susan K. Van Riper ; Griffin, Timothy J. ; Stone, Matthew D. ; Chilton, John ; Onsongo, Getiria ; Carlis, John V. |
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Zeitschrift: | PROTEOMICS, Jg. 10 (2010-09-07), S. 3533-3538 |
Veröffentlichung: | Wiley, 2010 |
Medientyp: | unknown |
ISSN: | 1615-9853 (print) |
DOI: | 10.1002/pmic.201000189 |
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