Segovia neXtProt update, 9 October 2014, Amos Bairoch

Stats are available for the Oct-2014 metrics except for HPA that will become available in Nov. (but in contexct of PE1 assignment, this is not affecting the missing protein list).

From the evolution of the missing protein lists from 2013 to 2014 we can see that shotgun approach is slowly leading to saturation. There is still room for a modest increase by going to some yet explored tissues and development stages or use targeted technology-driven strategies for example to explore membrane proteins.

But the rest of the missing proteins require specific targeted efforts that is highly dependent on the "type" of protein

The good thing is that many HPP groups are now accumulating evidence for the existence of a number of missing proteins.

These evidences are highly heterogenous but globally of a good quality.

The current way to get a neXtProt PE1 assignment is through litterature curation (UniProtKB/Swiss-Prot) or through presence in MS identification through PeptideAtlas MS data set reanalyis.

Therefore we need to open a new pipeline to validate proteins based on what we consider "nanopublications" (See Barend Mons et al, PMID:)

These nanopublications would be of the type:

Protein-X has_property "HPP-validated protein existence"

which would be linked to the:

source:

• The authors of the validation

experimental evidence:

• What type of experimental data allowed this confirmation (SRM, validated antibodies, RNASeq, etc).

biological model:

• What was the tissue(s)/cell line(s) used

Depending on the type of missing proteins, the evidence level will be different. Extraordinary claims will require solid evidence.

All this could be put in place during 2015 so that in the end of Aug/beginning of Sep 2015 a workshop would allow to review all the accumulated data and validate these nanopublications in time for the Vancouver meeting.