Converters

MaxQuant

Triqler contains functionality to convert MaxQuant output files into Triqler input files:

python -m triqler.convert.maxquant --file_list_file <file_list> <mq_evidence_file>

• <file_list> is a simple tab separated text file with spectrum file names in the first column and condition in the second column. The spectrum file names should be the same as in the "Raw file" column name in evidence.txt without the preceding path.
• <mq_evidence_file> is the file called evidence.txt present in the combined/txt folder of the MaxQuant results.

To obtain sufficient decoys, we recommended setting all FDR thresholds (PSM, peptide and protein-level) to 100% for best performance, though it usually also works with the default thresholds of 1% FDR.

Also note that MaxQuant uses the decoy prefix REV__ by default, so remember to call Triqler using this prefix:

triqler --decoy_pattern REV__ triqler_input.tsv

Currently, we have only tested this with matches-between-runs (MBR) turned off, as we still need to incorporate the error estimates from MaxQuant's MBR step, similar to what we have done with Quandenser (see below).

Quandenser

Triqler contains functionality to convert Quandenser output files into Triqler input files:

python -m triqler.convert.quandenser --file_list_file <file_list> --psm_files <percolator_target_psms_file>,<percolator_decoy_psms_file> <quandenser_feature_group_file>

• <file_list> is a simple text file with spectrum file names in first column and condition in second column.
• <percolator_target/decoy_psms_file> are the target/decoy PSM output files from Percolator. Both output files from stand-alone Percolator as well as from crux percolator are supported.
• <quandenser_feature_group_file> is the file called Quandenser.feature_groups.tsv in the Quandenser results folder.

DIA-NN

Triqler contains functionality to convert DIA-NN output files into Triqler input files:

python -m triqler.convert.diann --file_list_file <file_list> <diann_output_file>

• <diann_output_file> is a DIA-NN output file.
• <file_list> is a simple tab separated file with spectrum file names in first column and condition in second column.