ec-filter dataset

This contains two datasets used for demonstrate the dangers and solutions for post search filter in crosslinking mass-spectrometry. A dataset of search results for mycoplasma pneumonia acquisitions and escherichia coli. Both where searched against a combined database of all e.coli and mycoplasma pneumonia proteins.

These are results without any cut-off and are the base of testing if a filter or processing step is actually affecting decoys differently then target false positives. The idea being that these search results provide an decoy independent set of known false positive matches; all matches involving e.coli peptides to mycoplasma spectra and all matches involving mycoplasma pneumonia peptides to e.coli spectra. In the original use case the data where used to detect if a filter, that uses match external information to filter individual matches, results in an underrepresentation of decoys when compared to these secondary known false positives and how at least no contradiction was found when applying teh ec-filter style of applying the information.

The second dataset is a set of FDR results for 2% unique residue pair FDR of an yeast 26S Proteasome acquisition run with and without using the ec-filter and each of tzhese with and without xiFDR in built boosting. The spectra where searched against increasingly larger databases to show the effect of filtering the results depending on the database size – both in terms of present and assumed non-present proteins.