Galaxy |

OpenSwathWorkflow (version 3.1+galaxy0)

Input files separated by blank:

select mzml,mzxml,sqmass data sets(s)

transition file ('TraML','tsv','pqp'):

select pqp,tabular,traml data sets(s)

transition file ('TraML'):

select pqp,tabular,traml data sets(s)

additional nonlinear transition file ('TraML'):

select pqp,tabular,traml data sets(s)

Optional, tab-separated file containing the SWATH windows for extraction: lower_offset upper_offset:

Note that the first line is a header and will be skipped select txt data sets(s)

data is scanning SWATH data:

data is PASEF data:

Only extract RT around this value (-1 means extract over the whole range, a value of 600 means to extract around +/- 300 s of the expected elution):

Extraction window in ion mobility dimension (in 1/k0 or milliseconds depending on library):

This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side. -1 means extract over the whole range or ion mobility is not present. (Default for diaPASEF data: 0.06 1/k0)

Extraction window in Thomson or ppm (see mz_extraction_window_unit):

Extraction window used in MS1 in Thomson or ppm (see mz_extraction_window_ms1_unit):

Extraction window in ion mobility dimension for MS1 (in 1/k0 or milliseconds depending on library):

-1 means this is not ion mobility data

Parameters for the m/z and ion mobility calibrations

Parameters for the m/z and ion mobility calibration 0

Library parameters sections

Library parameters section 0

Parameters for the RTNormalization for iRT petides

Parameters for the RTNormalization for iRT petides 0

Scoring parameters sections

Scoring parameters section 0

Advanced Options

Advanced Options 0

Optional outputs: