Premium
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
Author(s) -
Scheri Richard C.,
Lee Junga,
Curtis Lawrence R.,
Barofsky Douglas F.
Publication year - 2008
Publication title -
rapid communications in mass spectrometry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.528
H-Index - 136
eISSN - 1097-0231
pISSN - 0951-4198
DOI - 10.1002/rcm.3719
Subject(s) - chemistry , isobaric labeling , electrospray ionization , chromatography , tandem mass spectrometry , mass spectrometry , ionization , proteome , analytical chemistry (journal) , desorption electrospray ionization , quadrupole , sample preparation , tandem , isobaric process , protein mass spectrometry , ion , chemical ionization , biochemistry , physics , materials science , organic chemistry , atomic physics , composite material , thermodynamics
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. Copyright © 2008 John Wiley & Sons, Ltd.