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OpenSwathRTNormalizer (version 3.1+galaxy0)

Run tool in batch mode for -in:

Input files separated by blank:

select mzml data sets(s)

transition file with the RT peptides ('TraML' or 'csv'):

select csv,traml data sets(s)

RT normalization file (how to map the RTs of this run to the ones stored in the library):

select trafoxml data sets(s)

Minimum r-squared of RT peptides regression:

Minimum relative amount of RT peptides to keep:

Whether the algorithms should try to choose the best peptides based on their peak shape for normalization:

Use this option you do not expect all your peptides to be detected in a sample and too many 'bad' peptides enter the outlier removal step (e.g. due to them being endogenous peptides or using a less curated list of peptides)

Parameters for the RTNormalizations

Parameters for the RTNormalization 0

Algorithm parameters sections

Algorithm parameters section 0

Parameters for the peptide estimation (use -estimateBestPeptides to enable)s

Parameters for the peptide estimation (use -estimateBestPeptides to enable) 0

Advanced Options

Advanced Options 0

Optional outputs:

This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space.

For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathRTNormalizer.html