The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays
Journal of Proteome Research, 2017
Schwenk J., Omenn G., Sun Z., Campbell D., Baker M., Overall C., Aebersold R., Moritz R., Deutsch E.
| Disease area | Application area | Sample type | Products |
|---|---|---|---|
Wider Proteomics Studies | Review/editorial |
Abstract
A review of the current status and progress of the HUPO Human Plasma Proteome Project (HPPP), which began in 2002 with the aim of establishing a comprehensive profile of the proteins present in human plasma in health and disease. This was conceived very much as a mass spec project, but is now starting to expand and explore additional complementary proteomic technologies. The earliest large compendium of plasma proteins was presented in 2002, describing 289 proteins in total, whereas in the latest HPPP “build” reported here, this number has risen to 3509.
The review touches on a number of important points, including the relatively small number of low/medium abundance proteins (based on RNA abundance) that have been detected during the largely mass spec-driven project. In 2009, these classes of proteins accounted for just 10% of those detected, which has now risen to ~23%. The specific difficulties of measuring lower-abundance proteins with MS is discussed in this context. There is an interesting section on the role of affinity-based technologies on the HPPP project. The discussion of immunoassays compared to MS is quite balanced and concludes with the statement, “In the long run, technologies that are capable of measuring proteins in multiplex and in a large number of samples will be beneficial for rapid analysis of plasma”. Another good quote is “The combination of these two technologies is probably underutilized today, having the potential to combine the sensitivity of affinity capture and specificity of MS, albeit still with the lower
speed of MS”. As well as protein abundance, the other stated issues for MS are sample volume and sample throughput.
There is also an overview of the major technologies available, and Olink gets a pretty good write-up in that regard in relation to the competition (see page 21 in the pdf). Overall, this should probably be viewed as essential reading in terms of the plasma proteome and our positioning with mass spec.