PeptideAtlas Measures 2013 Coverage of Kidney, Urine and Plasma Proteomes

Thanks to the diligent efforts of those involved in the Biology and Disease-driven Human Proteome Project, along with the Chromosome-centric Human Proteome Project, the year 2013 brought researchers closer to a complete picture of the urine, kidney and plasma proteomes.^{1, 2} Much of this work also stems from the Human Kidney & Urine Proteome Project and the Human Plasma Proteome Project initiatives.^3,4

The urine, kidney and plasma proteomes are interconnected through the body’s filtration system; numerous research groups have surveyed these proteomes in search of biomarkers of disease. Extending these findings along with protein data from the glomerulus and other regions of the kidney, Farrah et al. (2014) have compiled a PeptideAtlas build of this data, which boasts a larger protein coverage with higher-confidence protein identifications than any report published to date.⁵

The authors began by collecting data from experiments involving kidney, urine and plasma. They then constructed a PeptideAtlas build for each of the three sample types. Farrah and co-workers processed the data sets using a bioinformatics strategy based on the Trans-Proteomic Pipeline⁶; they also used spectral counting to estimate the relative protein abundances. Lastly, a bioinformatics pipeline made it possible to use the Peptide Atlas data sets to perform multi-pathway comparisons and Gene Ontology analysis.

The 2013 updated Human PeptideAtlas data sets have resulted in the addition of 4,005, 2,491 and 3,553 non-redundant proteins (with 1% FDR) to the kidney, urine and plasma proteomes, respectively. In addition, 12,644 non-redundant proteins and at least one peptide for each of the approximately 14, 000 Swiss-Prot entries are included in the build, an increase of approximately 7.5% of the predicted human proteome with respect to year 2012. The three PeptideAtlas builds (one each for kidney, urine and plasma) are available to other researchers through PeptideAtlas⁷ and have also been merged into neXtProt.⁸

References

1. Biology and Disease-driven Human Proteome Project.

2. Chromosome-centric Human Proteome Project.

3. Human Kidney & Urine Proteome Project.

4. Human Plasma Proteome Project.

5. Farrah,T., et al. (2014, January) “State of the Human Proteome in 2013 as Viewed through PeptideAtlas: Comparing the Kidney, Urine, and Plasma Proteomes for the Biology- and Disease-Driven Human Proteome Project,” Journal of Proteome Research, 13(1) (pp. 60–75), doi: 10.1021/pr4010037.

6. Deutsch, E., et al. (2010) “A guided tour of the Trans-Proteomic Pipeline,” Proteomics, 10(6) (pp. 1150–9).

7. Human Kidney, Urine and Plasma: PeptideAtlas builds.

8. Gaudet, P., et al. (2013) “neXtProt: Organizing protein knowledge in the context of human proteome projects,” Journal of Proteome Research, 12(1) (pp. 293−8).

Post Author: Emily Humphreys. As a biology undergraduate at the University of Utah, Emily balanced a heavy class schedule while working long hours in a lab studying eye development. Following graduation, she became involved in infectious disease and aging research involving SNPS.

While she enjoyed the thrill of research, Emily has since traded bench work for science journalism.
And has been a regular contributor to Accelerating Science since 2012.