Dataset Information

Human tissue microsomed by MRM, MRMHR and SWATH

ABSTRACT: The purpose of the present study was to examine simultaneously the absolute protein amounts of 152 membrane and membrane-associated proteins, including 30 metabolizing enzymes and 107 transporters, in pooled microsomal fractions of human liver, kidney and intestine by means of SWATH-MS with stable isotope-labeled internal standard peptides, and to compare the results with those obtained by MRM/SRM and high resolution (HR)-MRM/PRM.

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Sumio Ohtsuki

PROVIDER: PXD008265 | JPOST Repository | Mon Jan 01 00:00:00 GMT 2018

REPOSITORIES: jPOST

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Publications

Large-scale multiplex absolute protein quantification of drug-metabolizing enzymes and transporters in human intestine, liver, and kidney microsomes by SWATH-MS: Comparison with MRM/SRM and HR-MRM/PRM.

Nakamura Kenji K Hirayama-Kurogi Mio M Ito Shingo S Kuno Takuya T Yoneyama Toshihiro T Obuchi Wataru W Terasaki Tetsuya T Ohtsuki Sumio S

Proteomics 20160708 15-16

The purpose of the present study was to examine simultaneously the absolute protein amounts of 152 membrane and membrane-associated proteins, including 30 metabolizing enzymes and 107 transporters, in pooled microsomal fractions of human liver, kidney, and intestine by means of SWATH-MS with stable isotope-labeled internal standard peptides, and to compare the results with those obtained by MRM/SRM and high resolution (HR)-MRM/PRM. The protein expression levels of 27 metabolizing enzymes, 54 tra ...[more]

PMID: 27197958

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Project description:The current state of proteomics requires a choice between targeted and discovery methods. The former provides exceptional quantitation and data completeness, but only with few analytes. Discovery proteomics can identify hundreds and thousands of proteins in a sample, but with poor quantitation and data completeness. We have established and optimized a method that combines targeted and data-independent acquisition for absolute quantitation of all plasma proteins in a single sequential window acquisition of all theoretical fragment ions (SWATH) acquisition run using a panel of spike-in standards (SIS). We compared the absolute quantitation (AQ) of SWATH and high-resolution multiple-reaction monitoring (MRM-HR) acquisition methods using the 100 protein PlasmaDive SIS panel spiked into human plasma. SWATH provided equivalent quantitation and differentially abundant protein profiles as MRM-HR. Absolute quantities of the SIS peptides from the SWATH data were used to estimate the absolute quantities (eAQ) for all the proteins in the run. The eAQ values provided similar quantitation and differentially abundant protein profiles as AQ and protein group (PG) values, and the eAQ method was the only scheme where all selected proteins were verified by MRM-HR. We applied the eAQ method to a cohort of 16 non-small cell lung cancer (NSCLC) patients receiving immunotherapeutics and found that fibronectin (FN1) and proteoglycan 4 (PRG4) were useful markers for predicting patients who would stay on these agents for at least 6 months (area under the curve of 0.8438 and 0.6735, respectively). Thirteen additional plasma samples confirmed that FN1 and PRG4 are putative biomarkers (positive predictive value is 100% and 85.7%, respectively) for a prolonged (>6 months) response to immunotherapeutic agents. In conclusion, we describe an optimized method for absolute quantification of all proteins in a SWATH run, and this approach is amenable for the identification of plasma biomarkers.

Dataset Information

Human tissue microsomed by MRM, MRMHR and SWATH

Publications

Large-scale multiplex absolute protein quantification of drug-metabolizing enzymes and transporters in human intestine, liver, and kidney microsomes by SWATH-MS: Comparison with MRM/SRM and HR-MRM/PRM.

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