title: A comparison of relative quantification with isobaric tags on a subset of the murine hepatic proteome using electrospray ionization quadrupole time-of-flight and matrix-assisted laser desorption/ionization tandem time-of-flight.
abstract: The use of isobaric tagging for relative and absolute quantification (iTRAQ) has increased dramatically over the past few years. Many factors can affect the accuracy of quantification. Some of these include the number of biological/technical replicates, sample complexity, instrumentation, method of peptide/protein identification and the statistical techniques used for data analysis. It has been observed that the low collision energies normally used in electrospray ionization quadrupole time-of-flight (ESI QTOF) can result in low iTRAQ reporter ion abundances. We used two-way analysis of variance (ANOVA) to compare the iTRAQ ratios that were generated on an ESI QTOF and a matrix-assisted laser desorption/ionization tandem time-of-flight (MALDI TOF/TOF). It appears that iTRAQ analyses performed on an ESI QTOF without any special modifications to instrumental parameters produce essentially the same protein ratios as those obtained on a MALDI TOF/TOF.
authors.affiliation: Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA. scherir@onid.orst.edu
authors.forename: Richard C
authors.initials: RC
authors.lastname: Scheri
authors.forename: Junga
authors.initials: J
authors.lastname: Lee
authors.forename: Lawrence R
authors.initials: LR
authors.lastname: Curtis
authors.forename: Douglas F
authors.initials: DF
authors.lastname: Barofsky
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D007631:Chlordecone / Q000737:chemistry; D002784:Cholesterol / Q000097:blood; D003627:Data Interpretation, Statistical; D016208:Databases, Factual; D007202:Indicators and Reagents; D008099:Liver / Q000737:chemistry*; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D008969:Molecular Sequence Data; D020543:Proteome / Q000737:chemistry*; D013050:Spectrometry, Fluorescence; D021241:Spectrometry, Mass, Electrospray Ionization; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D007202:Indicators and Reagents; D020543:Proteome; D002784:Cholesterol; D007631:Chlordecone
references.citation: Methods. 2003 Feb;29(2):124-30
references.pmid: 12606218
references.citation: J Proteome Res. 2004 May-Jun;3(3):350-63
references.pmid: 15253416
references.citation: Mol Cell Proteomics. 2005 Mar;4(3):255-66
references.pmid: 15632418
references.citation: J Proteome Res. 2005 Mar-Apr;4(2):377-86
references.pmid: 15822913
references.citation: Proteomics. 2005 Jun;5(9):2297-308
references.pmid: 15887184
references.citation: Mol Cell Proteomics. 2004 Dec;3(12):1154-69
references.pmid: 15385600
references.citation: J Proteome Res. 2008 Mar;7(3):897-907
references.pmid: 18232632
references.citation: Drug Metab Dispos. 1989 Mar-Apr;17(2):131-8
references.pmid: 2468465
references.citation: Mol Biol Cell. 2007 Apr;18(4):1507-18
references.pmid: 17314409
references.citation: Drug Metab Dispos. 1991 May-Jun;19(3):673-8
references.pmid: 1717217
references.citation: Proteomics. 2007 Feb;7(3):340-50
references.pmid: 17177251
references.citation: Nat Biotechnol. 1999 Oct;17(10):994-9
references.pmid: 10504701
references.citation: Toxicol Appl Pharmacol. 2008 Jun 15;229(3):265-72
references.pmid: 18387646
references.citation: Biomed Environ Mass Spectrom. 1988 Oct;16(1-12):99-111
references.pmid: 3072035
references.citation: Proteomics. 2006 Aug;6(15):4321-34
references.pmid: 16800037
references.citation: Proteomics. 2005 Jan;5(1):4-15
references.pmid: 15602776
references.citation: J Proteome Res. 2006 Mar;5(3):589-98
references.pmid: 16512674