Input File Examples
The standard input filetype is the tab delimited output from the percolator algorithm. Please see below for examples of input files:
Standard Percolator Output
Target Output
| PSMid | score | q-value | posterior_error_prob | peptide | proteinIds | |||
|---|---|---|---|---|---|---|---|---|
| 1.1 | 7.5 | 0.0048 | 0.0007 | R.NYIQSLTQMPK.M | MK14_HUMAN|Q16539 | MK14_HUMAN|Q16539-2 | MK14_HUMAN|Q16539-3 | |
| 1.2 | 6.2 | 0.0035 | 0.0006 | R.NTVASSSRSM*R.T | FHDC1_HUMAN|Q9C0D6 |
Decoy Output
| PSMid | score | q-value | posterior_error_prob | peptide | proteinIds | |||
|---|---|---|---|---|---|---|---|---|
| 1.1 | 1.3 | 0.18 | 0.27 | R.RSTITSRE.M | decoy_MK14_HUMAN|Q16539 | decoy_MK14_HUMAN|Q16539-2 | decoy_MK14_HUMAN|Q16539-3 | |
| 1.2 | 0.9 | 0.35 | 0.36 | R.KKRKRSRKEM*R.T | decoy_FHDC1_HUMAN|Q9C0D6 |
Decoy proteins should have some sort of decoy identifier to distinguish between target and decoy proteins. This is typically "decoy_" or "##". See the decoy symbol parameter option here for more information. These can also be combined into one file called "Combined Output".
With the above standard input one could use q-value or posterior_error_prob as the PSM score. See Score Section of the parameter file explanation with multiplicative as psm_score_type and any of the multiplicative options for protein_score.
For example standard input files please see any of the following files from the our repository:
tests/data/test_perc_data_target.txttests/data/test_perc_data_decoy.txt
Custom Input
| PSMid | custom_score | peptide | proteinIds | |
|---|---|---|---|---|
| 1.1 | 7.5 | R.NYIQSLTQMPK.M | MK14_HUMAN|Q16539 | MK14_HUMAN|Q16539-2 |
| 1.2 | 6.2 | R.NTVASSSRSM*R.T | FHDC1_HUMAN|Q9C0D6 |
With the above custom input one could use custom_score as the PSM psm_score with additive as the psm_score_type and protein_score.
For example custom input files please see any of the following files from the our repository:
tests/data/test_perc_data_target_additive.txttests/data/test_perc_data_decoy_additive.txttests/data/test_perc_data_target_multiplicative.txttests/data/test_perc_data_decoy_multiplicative.txt
Fasta File
This package was developed using standard Fasta files from Uniprot. Please see an example entry in a Fasta database below:
>sp|Q5QNW6|H2B2F_HUMAN Histone H2B type 2-F OS=Homo sapiens OX=9606 GN=H2BC18 PE=1 SV=3
MPDPAKSAPAPKKGSKKAVTKVQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSSK