This tool demonstrates the search-all-asses-subset method to control
the False Discovery Rate (FDR) when you are only interested in a subset
of the identified PSMs from a shotgun proteomics experiment.
The workflow is as follows:
- search spectra against all expected proteins
- Remove PSMs from irrelevant proteins
- Calculate FDR
You can load the data from step 1. into this webtool to perform
step 2. and 3.
Use the Browse… button above to load a CSV file from your computer
or paste the data in the text area to the right.
Adhere to the following format:
- Every Row is a unique PSM
- Every row contains:
- id: Can be any text or number
- score: Score given to the PSM, higher scores are better
- decoy: FALSE or TRUE; TRUE indicates that the PSM matches a decoy peptide sequence
- subset: FALSE or TRUE: TRUE indicates that the PSM matches a subset peptide sequence
- The first row are the column names
- All columns should be comma separated
Note that the row with extra set of decoys (decoy = TRUE and subset = FALSE) are not necessarily the non-subset decoys from the same mass spectrometry run but can be chosen by the user.
Example input:
id,score,decoy,subset
1,7.67,TRUE,FALSE
2,10.99,TRUE,TRUE
3,75.10,FALSE,FALSE
4,73.83,FALSE,TRUE
Warning: use this tool only with PSMs from a competitive target-decoy search!
The minimal required input are PSMs from subset targets and decoys (row 2 and 4 in example input).
Additional decoy PSMs (row 1) are used for a more stable FDR calculation.
Non subset targets (row 3) are ignored in the analysis.