HDL Proteome Watch:
Current official count: 251 proteins*
*defined as appearing in 3 separate reports from 3 independent laboratories (from 45 studies surveyed).
HDL is not just one thing. Unbiased proteomic studies are showing that HDL contains numerous proteins and lipids that segregate into distinct subclasses. As a result of differences in instruments, sensitivity, HDL isolation technique, patient donors etc., the total "list" of HDL proteins can vary dramatically from study to study. To try to make sense of this, we have consolidated all existing data so that a more realistic estimate of the HDL proteome can be determined. We compared some 40 different proteomics studies that, 1) used modern mass spectrometry proteomics techniques, 2) studied HUMAN HDL samples isolated by a variety of techniques, and 3) made their raw data publically available or were willing to send it to us.
The spreadsheet is in Excel format (see link below) and is freely available to the scientific community. The identified proteins have been hyperlinked to the Uniprot Protein Knowledgebase so that the details and functions of each protein can be easily accessed.
We have strived to maintain an unbiased approach to the data. Our list includes many proteins such as skin keratins and immunoglobulins that many investigators dismiss as contaminants. Our philosophy has been to compile ALL identifications and let users define for themselves what proteins to emphasize.
We encourage you to use the list and cite it if you like. You don't have to cite our lab. If you feel we have left something out, please contact Sean Davidson. We will update the list as quickly and frequently as possible.
Gene Ontology Analysis of the "consensus" HDL proteins:
Frequency of observation of each consensus HDL protein:
Download the database here