title: Impact of Sample Matrix on Accuracy of Peptide Quantification: Assessment of Calibrator and Internal Standard Selection and Method Validation.
abstract: Protein quantification based on peptides using LC-MS/MS has emerged as a promising method to measure biomarkers, protein drugs, and endogenous proteins. However, the best practices for selection, optimization, and validation of the quantification peptides are not well established, and the influence of different matrices on protein digestion, peptide stability, and MS detection has not been systematically addressed. The aim of this study was to determine how biological matrices affect digestion, detection, and stability of peptides. The microsomal retinol dehydrogenase (RDH11) and cytosolic soluble aldehyde dehydrogenases (ALDH1As) involved in the synthesis of retinoic acid (RA) were chosen as model proteins. Considerable differences in the digestion efficiency, sensitivity, and matrix effects between peptides were observed regardless of the target protein's subcellular localization. The precision and accuracy of the quantification of RDH11 and ALDH1A were affected by the choice of calibration and internal standards. The final method using recombinant protein calibrators and stable isotope labeled (SIL) peptide internal standards was validated for human liver. The results demonstrate that different sample matrices have peptide, time, and matrix specific effects on protein digestion and absolute quantification.
authors.affiliation: Department of Pharmaceutics, University of Washington , Health Science Building, Room H-272M, Box 357610, Seattle, Washington 98195-7610, United States.
authors.forename: Samuel L
authors.initials: SL
authors.lastname: Arnold
authors.affiliation: Department of Pharmaceutics, University of Washington , Health Science Building, Room H-272M, Box 357610, Seattle, Washington 98195-7610, United States.
authors.forename: Faith
authors.initials: F
authors.lastname: Stevison
authors.affiliation: Department of Pharmaceutics, University of Washington , Health Science Building, Room H-272M, Box 357610, Seattle, Washington 98195-7610, United States.
authors.forename: Nina
authors.initials: N
authors.lastname: Isoherranen
mesh_terms: D000444:Aldehyde Dehydrogenase / Q000032:analysis* / Q000378:metabolism / Q000592:standards; D000080924:Aldehyde Dehydrogenase 1 Family; D002138:Calibration; D002851:Chromatography, High Pressure Liquid; D006801:Humans; D007553:Isotope Labeling / Q000592:standards; D008099:Liver / Q000378:metabolism; D010088:Oxidoreductases / Q000032:analysis* / Q000378:metabolism / Q000592:standards; D010455:Peptides / Q000032:analysis* / Q000378:metabolism / Q000592:standards; D012015:Reference Standards; D050697:Retinal Dehydrogenase; D053719:Tandem Mass Spectrometry
chemical_list: D010455:Peptides; D010088:Oxidoreductases; C422653:RDH11 protein, human; D000080924:Aldehyde Dehydrogenase 1 Family; D000444:Aldehyde Dehydrogenase; C510223:ALDH1A1 protein, human; D050697:Retinal Dehydrogenase