Integrated quantification method for protein measurements in clinical proteomics

摘要

Methods are provided for determining the expression level of target proteins in a subject. A plurality of respective peptide transitions are generated from a plurality of proteins obtained from a biological sample from the subject, wherein the plurality of proteins comprises both target and normalizing proteins. A mass spectroscopy (MS) signal intensity is measured from the plurality of respective peptide transitions and a plurality of corresponding stable isotope-labeled internal standard (SIS) peptide transitions. For each of the plurality of proteins, a response ratio is calculated between the MS signal intensity of the respective peptide transition and the corresponding SIS peptide transition. The response ratio for each target protein is normalized by a sample-dependent normalization factor calculated from the response ratio for each normalizing protein, wherein the normalized response ratios provide a determination of the expression level of the target proteins.

主权项

1. A method for determining the expression level of target proteins in a subject, comprising:
generating a plurality of respective peptide transitions from a plurality of proteins obtained from a biological sample from the subject, wherein the plurality of proteins comprises both target and normalizing proteins; measuring a mass spectroscopy (MS) signal intensity from the respective plurality of peptide transitions and a plurality of corresponding stable isotope-labeled internal standard (SIS) peptide transitions; for each of the plurality of proteins, calculating a response ratio between the MS signal intensity of the peptide transition and the corresponding SIS peptide transition; calculating a sample-dependent normalization factor from the response ratios for the normalizing proteins; wherein the normalizing proteins are selected based on their ability to reduce intensity drift (D) of each of the plurality of respective peptide transitions, wherein intensity drift determines the deviation in abundance of each peptide transition from the overall median abundance of each peptide transition and normalizing the response ratio for each target protein by the sample-dependent normalization factor, wherein the normalized response ratios provide a determination of the expression level of the target proteins.