Patent ID: 8187893
Filing Date: 2012-05-29
Classification: G01N,Y10T

Abstract:
1. A mass spectrometric based assay for presence of a protein in a sample without the use of a standard for the protein, comprising the steps of: predicting one or more of the proteolytic fragments of a protein based on one or more of an amino acid sequence for the protein and a translation of a gene sequence for the protein; predicting one or more of the fragments produced from one or more of the proteolytic fragments of the protein when the proteolytic fragment is subjected to collision induced dissociation; measuring the ion signal of the m/z value range encompassing one or more of the predicted collision induced dissociation fragments m/z value using said multiple reaction monitoring; performing a substantially full product ion scan on a m/z value range encompassing a predicted proteolytic fragment m/z value when the measured ion signal corresponding to one or more collision induced dissociation fragments of the predicted proteolytic fragment is above a specified signal threshold; measuring the ion signals associated with the parent-daughter ion transitions of said substantially full product ion scan; selecting as the parent-daughter ion transition for an assay of the presence of the protein in a sample a parent-daughter ion transition of said substantially full product ion scan, wherein the selected parent-daughter ion transition for the assay corresponds to a transition where the transmitted parent ion is a proteolytic fragment of said protein, and wherein the selected parent-daughter ion transition has, relative to the measured ion signals associated with the other parent-daughter ion transitions for said protein, one or more of the approximately highest ion signal and the approximately highest signal-to-noise ratio; and refining the selection of the predicted collision induced dissociation fragments of the predicted proteolytic fragments based on at least one or more of the measured full product ion scans; subjecting at least a portion of the eluent from the chromatographic column to multiple reaction monitoring, the transmitted parent ion m/z range of each multiple reaction monitoring scan including a m/z value of one or more of the refined daughter ion m/z range of each multiple reaction monitoring scan including a m/z value of one or more of the refined predicted collision induced dissociation fragments of the predicted proteolytic fragments; and measuring the ion signal of the m/z value range encompassing one or more of the refined predicted collision induced dissociation fragments m/z value using said multiple reaction monitoring.