Patent ID: 8633031
Filing Date: 2014-01-21
Classification: G01N

Abstract:
1. A method for determining the concentration of one or more proteins of interest in two or more samples of interest using parent-daughter ion transition monitoring (PDITM) in mass spectrometry, comprising the steps of: providing an internal standard sample for each of the one or more proteins of interest, each internal standard sample comprising a signature peptide having a sequence that uniquely identifies each corresponding protein of interest; labeling the signature peptide with a chemical moiety comprising either subjecting the labeled internal standard sample to PDITM; selecting a diagnostic daughter ion for each labeled signature peptide; labeling the one or more proteins of interest in two or more samples of interest, separately, with the chemical moiety comprising either to generate two or more labeled samples of interest, the two or more labeled samples of interest thereby being differentially labeled with respect to the labeled internal standard sample; combining, to produce two or more combined samples, at least a portion of the one or more labeled internal standard samples with at least a portion of each of two or more differentially labeled samples of interest; loading at least a portion of each combined sample on a chromatographic column; eluting at least a portion of the combined sample from the chromatographic column to generate an eluent containing signature peptides wherein heavy and light signature peptides are co-eluting or wherein isobaric tagged signature peptides are co-eluting, respectively; subjecting at least a portion of the eluent from the chromatographic column to PDITM, wherein (i) a transmitted parent ion m/z range of each PDITM scan includes a m/z value of one or more of the labeled signature peptides and (ii) a transmitted daughter ion m/z range of each PDITM scan includes a m/z value of one or more of the selected diagnostic daughter ions corresponding to the transmitted labeled signature peptide; measuring the ion signal of one or more of the selected diagnostic daughter ions using said PDITM; and determining the concentration of one or more proteins of interest in the two or more samples of interest by comparing the measured ion signal of a selected diagnostic daughter ion corresponding to the protein of interest from a sample of interest to the measured ion signal for the selected diagnostic daughter ion corresponding to the protein of interest from a labeled internal standard sample wherein, optionally, the combining step is preceded, followed, or both preceded and followed by digesting protein of each sample or of the combined sample to generate peptides.