I ran a test with one file and got 1898 peptide IDs but there are only 1691 peptides in the "common_peptides.csv" file. We should be getting quantities for all 1898 peptides. If we want to ignore the 18 decoys that is fine, so that would be 1880 peptides, meaning we are still missing 189 peptides or about 10%.
I ran a test with one file and got 1898 peptide IDs but there are only 1691 peptides in the "common_peptides.csv" file. We should be getting quantities for all 1898 peptides. If we want to ignore the 18 decoys that is fine, so that would be 1880 peptides, meaning we are still missing 189 peptides or about 10%.
Here is the mzXML file I used to test:
20200719_MAGIC_MCF7_1128repro_70.zip
Peptide FDR output:
CsoDIAq-file1_20200719_MAGIC_MCF7_1128repro_70_corrected_peptideFDR.csv
"common_peptides.csv" common_peptides.csv
Also minor there is no column name for the file for some reason?