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.
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.
Scheri
Richard C
RC
Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA. scherir@onid.orst.edu
Lee
Junga
J
Curtis
Lawrence R
LR
Barofsky
Douglas F
DF
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
D007202:Indicators and Reagents; D020543:Proteome; D002784:Cholesterol; D007631:Chlordecone
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