This thread continues the discussion in #1027. As part of the protein inference beta testing, we aim to reproduce roughly the results from a TPP protein quantification published in [1]. Even with a working FidoAdapter, there remain some other issues to be resolved and optimised.

In the test dataset, a wild type (wt) mouse skin sample is compared to a Cathepsin L knockout (Ctsl-/-). The two samples were dimethyl labelled heavy (+34Da) and light (+28Da) respectively, mixed and then split into eleven fractions ST366 to ST376.

The aim is to roughly re-produce the protein list of the TPP analysis. Many of the high intensity proteins have been checked independently by Western Blotting.

[1] Tholen et al. CMLS 71(5), 899–916 (Mar. 2014). http://www.ncbi.nlm.nih.gov/pubmed/23233448