A Simple Protocol To Routinely Assess the Uniformity of Proteomics Analyses

Mass-spectrometry-based
proteomic approaches are increasingly applied
to biological and clinical studies. Initially used by specialized
laboratories, the technology has matured and gained acceptance by
the community, using various analytical processes and platforms. To
facilitate data comparison and integration across laboratories, there
is a need to harmonize analytical processes to ensure the generation
of reliable proteomic data sets. This is especially critical in the
context of large initiatives, such as the Human Proteome Project promoted by the Human Proteome Organization (HUPO). Quality control
is a first step toward the harmonization of proteomics data sets.
We have developed a procedure to routinely assess the uniformity of
proteomics analyses. It relies on a simple protocol based on three
proteins and two sets of isotopically labeled peptides, one being
added prior to tryptic digestion and the second one prior to liquid
chromatography–mass spectrometry (LC–MS) analysis. The
proposed method evaluates in a single step both the sample preparation,
by measuring the relative amounts of endogenous peptides and their
isotopically labeled counterparts, and the LC–MS platform performance,
by monitoring the main LC–MS attributes for reference peptides.
The procedure is simple and easy to implement into routine workflows
typically employed by the proteomics community.