Antibody-free processes are disclosed that provide accurate quantification of a wide variety of low-abundance target analytes in complex samples. The processes can employ high-pressure, high-resolution chromatographic separations for analyte enrichment. Intelligent selection of target fractions may be performed via on-line Selected Reaction Monitoring (SRM) or off-line rapid screening of internal standards. Quantification may be performed on individual or multiplexed fractions. Applications include analyses of, e.g., very low abundance proteins or candidate biomarkers in plasma, cell, or tissue samples without the need for affinity-specific reagents.
STATEMENT REGARDING RIGHTS TO INVENTION MADE UNDER FEDERALLY-SPONSORED RESEARCH AND DEVELOPMENT
 This invention was made with Government support under the National Institutes of Health (NIH) Director's New Innovator Program Award Number DP2OD006668, NIH Grant Numbers 8P41-GM103493, 5P41-RR018522, CA111244, and U24-CA-160019, National Cancer Institute (NCI) Early Detection Research Network Interagency Agreement Number Y01-CN-05013-29, and Contract Number DE-AC05-76RLO-1830 awarded by the U.S. Department of Energy. The Government has certain rights in the invention.