Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification.

Mol Cell Proteomics
Authors
Keywords
Abstract

Verification of candidate biomarker proteins in blood is typically done using multiple reaction monitoring (MRM) of peptides by LC-MS/MS on triple quadrupole MS systems. MRM assay development for each protein requires significant time and cost, much of which is likely to be of little value if the candidate biomarker is below the detection limit in blood or a false positive in the original discovery data. Here we present a new technology, accurate inclusion mass screening (AIMS), designed to provide a bridge from unbiased discovery to MS-based targeted assay development. Masses on the software inclusion list are monitored in each scan on the Orbitrap MS system, and MS/MS spectra for sequence confirmation are acquired only when a peptide from the list is detected with both the correct accurate mass and charge state. The AIMS experiment confirms that a given peptide (and thus the protein from which it is derived) is present in the plasma. Throughput of the method is sufficient to qualify up to a hundred proteins/week. The sensitivity of AIMS is similar to MRM on a triple quadrupole MS system using optimized sample preparation methods (low tens of ng/ml in plasma), and MS/MS data from the AIMS experiments on the Orbitrap can be directly used to configure MRM assays. The method was shown to be at least 4-fold more efficient at detecting peptides of interest than undirected LC-MS/MS experiments using the same instrumentation, and relative quantitation information can be obtained by AIMS in case versus control experiments. Detection by AIMS ensures that a quantitative MRM-based assay can be configured for that protein. The method has the potential to qualify large number of biomarker candidates based on their detection in plasma prior to committing to the time- and resource-intensive steps of establishing a quantitative assay.

Year of Publication
2008
Journal
Mol Cell Proteomics
Volume
7
Issue
10
Pages
1952-62
Date Published
2008 Oct
ISSN
1535-9484
URL
DOI
10.1074/mcp.M800218-MCP200
PubMed ID
18534968
PubMed Central ID
PMC2559937
Links
Grant list
U01 HL081341 / HL / NHLBI NIH HHS / United States
U24 CA126476 / CA / NCI NIH HHS / United States
1U24 CA126476-02 / CA / NCI NIH HHS / United States
U01-HL081341 / HL / NHLBI NIH HHS / United States