Finding proteins that hit the mark

Unbiased Discovery Platform

Since its incorporation in 2000, Caprion has been using its unbiased discovery platform to support our partners’ biomarker and target discovery efforts. Our proteomics team has developed robust, industrialized procedures to ensure high quality, reproducible results.

Caprion’s unbiased discovery workflow uses LC-MS/MS to analyze the proteome of large numbers of samples in order to identify proteins (e.g. biomarkers or targets) which exhibit differential expression between study cohorts. Advantages of this approach include:

  • Hypothesis-free approach promotes novel findings
  • Compatibility with a wide range of sample matrices
  • Simultaneous identification and relative quantitation of proteins
  • Industrialized process can analyze 1000s of proteins across 100s of samples.

The discovery workflow is outlined below.


Proteins are digested with trypsin or other enzymes (1) to generate peptides and may undergo further fractionation (2), depending on sample complexity and study goals.

Peptides are analyzed in scanning (LC-MS) mode (3) generating a 3D map whereby each peptide is assigned a retention time, an m/z value and an intensity value. These maps, which track up to 50,000 peptides per sample, are aligned across samples (4). Statistical analyses are then performed to identify which peptides differ between study groups of interest (5).

In parallel, the peptides are subjected to tandem mass spectrometry (LC-MS/MS) whereby peptides are fragmented into smaller ions (6). These fragmentation spectra are matched to predicted spectra from well-characterized databases (7).

This process yields identification and relative quantitation of thousands of peptides, which are then subjected to bioinformatics and biostatistical analysis to yield putative biomarkers or targets (8).

© 2017 Caprion