title: LTQ-iQuant: A freely available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from LTQ instruments.
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.
authors.affiliation: Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.
authors.forename: Getiria
authors.initials: G
authors.lastname: Onsongo
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Stone
authors.forename: Susan K
authors.initials: SK
authors.lastname: Van Riper
authors.forename: John
authors.initials: J
authors.lastname: Chilton
authors.forename: Baolin
authors.initials: B
authors.lastname: Wu
authors.forename: Leeann
authors.initials: L
authors.lastname: Higgins
authors.forename: Troy C
authors.initials: TC
authors.lastname: Lund
authors.forename: John V
authors.initials: JV
authors.lastname: Carlis
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Griffin
mesh_terms: D010455:Peptides / Q000032:analysis; D011506:Proteins / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D012984:Software; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods
chemical_list: D010455:Peptides; D011506:Proteins
references.citation: J Proteome Res. 2006 Sep;5(9):2328-38
references.pmid: 16944945
references.citation: Mol Cell Proteomics. 2010 Sep;9(9):1885-97
references.pmid: 20382981
references.citation: Mol Cell Proteomics. 2008 Sep;7(9):1702-13
references.pmid: 18511480
references.citation: J Am Soc Mass Spectrom. 2008 Sep;19(9):1255-62
references.pmid: 18620867
references.citation: Proteomics. 2007 Apr;7(7):1150-63
references.pmid: 17390297
references.citation: BMC Genomics. 2005 Oct 20;6:145
references.pmid: 16242023
references.citation: J Am Soc Mass Spectrom. 2009 Aug;20(8):1425-34
references.pmid: 19403316
references.citation: Mol Cell Proteomics. 2010 May;9(5):780-90
references.pmid: 20019052
references.citation: J Proteome Res. 2007 Nov;6(11):4200-9
references.pmid: 17902639
references.citation: J Am Soc Mass Spectrom. 2009 Jul;20(7):1287-302
references.pmid: 19345114
references.citation: J Proteome Res. 2008 Sep;7(9):3643-8
references.pmid: 18646790
references.citation: Mol Cell Proteomics. 2004 Dec;3(12):1154-69
references.pmid: 15385600
references.citation: Chembiochem. 2005 Nov;6(11):1941-51
references.pmid: 16206229
references.citation: Anal Chem. 2003 Apr 15;75(8):1895-904
references.pmid: 12713048
references.citation: Proteomics. 2009 Jun;9(12):3328-40
references.pmid: 19504495
references.citation: Nat Biotechnol. 2007 Sep;25(9):1035-44
references.pmid: 17721511