title: Increased quantitative proteome coverage with (13)C/(12)C-based, acid-cleavable isotope-coded affinity tag reagent and modified data acquisition scheme.
abstract: Quantitative protein profiling using the isotope-coded affinity tag (ICAT) method and tandem mass spectrometry (MS) enables the pair-wise comparison of protein expression levels in biological samples. A new version of the ICAT reagent with an acid-cleavable bond, which allows removal of the biotin moiety prior to MS and which utilizes (13)C substitution for (12)C in the heavy-ICAT reagent rather than (2)H (for (1)H) as in the original reagent, was investigated. We developed and validated an MS data acquisition strategy using this new reagent that results in an increased number of protein identifications per experiment, without losing the accuracy of protein quantification. This was achieved by following a single survey (precursor) ion scan and serial collision induced dissociations (CIDs) of four different precursor ions observed in the prior survey scan. This strategy is common to many high-performance liquid chromatography-electrospray ionization (HPLC-ESI)-MS shotgun proteomic strategies, but heretofore not to ICAT experiments. This advance is possible because the new ICAT reagent uses (13)C as the "heavy" element rather than (2)H, thus, eliminating the slight delay in retention time of ICAT-labeled "light" peptides on a C18-based HPLC separation that occurs with (2)H and (1)H. Analyses using this new scheme of an ICAT-labeled trypsin-digested six protein mixture as well as a tryptic digest of a total yeast lysate, indicated that about two times more proteins were identified in a single analysis, and that there was no loss in accuracy of quantification.
authors.affiliation: Institute for Systems Biology, Seattle, WA 98103, USA. eyi@systemsbiology.org
authors.forename: Eugene C
authors.initials: EC
authors.lastname: Yi
authors.forename: Xiao-Jun
authors.initials: XJ
authors.lastname: Li
authors.forename: Kelly
authors.initials: K
authors.lastname: Cooke
authors.forename: Hookeun
authors.initials: H
authors.lastname: Lee
authors.forename: Brian
authors.initials: B
authors.lastname: Raught
authors.forename: Andrew
authors.initials: A
authors.lastname: Page
authors.forename: Victoria
authors.initials: V
authors.lastname: Aneliunas
authors.forename: Phil
authors.initials: P
authors.lastname: Hieter
authors.forename: David R
authors.initials: DR
authors.lastname: Goodlett
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D002244:Carbon / Q000737:chemistry; D002247:Carbon Isotopes / Q000737:chemistry*; D002852:Chromatography, Ion Exchange; D019075:Electrophoresis, Capillary; D007202:Indicators and Reagents / Q000737:chemistry*; D007553:Isotope Labeling; D007554:Isotopes / Q000737:chemistry; D013058:Mass Spectrometry; D040081:Protein Array Analysis; D011506:Proteins / Q000378:metabolism; D020543:Proteome / Q000032:analysis*; D015203:Reproducibility of Results; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D014357:Trypsin / Q000378:metabolism
chemical_list: D002247:Carbon Isotopes; D007202:Indicators and Reagents; D007554:Isotopes; D011506:Proteins; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; D002244:Carbon; D014357:Trypsin