Output file type

[BaylorSci]

I recently read in a manuscript that it is possible to get mgf output from IMTBX / Grppr which can subsequently be converted to mzXML and wondered how that is accomplished? Specifically the output in mgf form. While i can successfully output a file with the same name as the input file via GUI, the outputted processed raw file is not readable by msconvert. I have tried the --allOut which is supposed to be found in the GUI (version 5.0.1) or on the command line, however i am told that this option -allOut is unknown. Any help would be very much appreciated.

[chhh]

@BaylorSci
Generation of MGF is done by the Grppr part of the program. It is trigggered by checking the box "Precursor-fragment grouping" at the bottom of the UI. It corresponds to the --fmt option of Grppr:

IMTBX_v5.0.1 $ java -jar .\grppr-0.3.21.jar
Grppr (0.3.21) - deisotoping and precursor/fragment grouping

The program creates pseudo MS/MS spectra from features detected in Ion Mobility data from
    Waters instruments, such as Synapt G2-Si.

Author: Dmitry Avtonomov (Nesvizhskii lab, University of Michigan, 2016-2020)

Usage: java -jar -Xmx2G grppr.jar [options]
  Options:
    --allOut
      When set, will write *.isotopes files even during precursor fragment
      grouping
      Default: false
...
    --fmt
      Output file format for grouping precursors and fragments (see '--group'
      option). Only MGF is supported for now.
      Default: MGF
      Possible Values: [MGF]
....

You have to set Operation Mode to ScanByScan (that's the LCMS processing mode). I don't remember at this point if Output Format has to be set to ScanMetaInfo or if other formats are also supported.

Here's an example of configuration in the GUI that I just tried out (limited to 100 scans). Note that I used "+" sign in the output directory to specify that it's relative to the root directory of data. So in this case results will be placed inside a subdirectory "results_mgf" in the data raw data directory. You can use an absolute path as well:

If you click "Commands" you can see exactly what will be executed under the hood:

Note that in the following commands you should use the actual paths/names of 'IMTBX.exe' and 'grppr.jar' as found on your computer after unpacking the release archive.

IMTBX.exe peaks -vw --bounds_im 0 0 --bounds_mz 0 0 --clean True --cut 30 --digits 5 3 1 4 --drop 0.1 --filter 2 2 2 2 1 1 --hyper 0.4 0.3 0.49 -i D:\ms-data\waters\some-waters.raw --imsr 20 0 100 --index True --lock True --lockmass 785.8426 0.5 --locksmooth 10 --max 1599 --min 1500 -n True --noise True --noiseWnd 2 6 --npts 9 --npts1d 3 -o +results_mgf --orig --scansPerThread 1 --threads 1 --tol 0.01

java -jar grppr.jar --dSnr 0.5 1.0 --isoAlg AVERAGINE --isoMzV 30.0 --isoMzT PPM --isoTi 2.0 -g True -d 1 2 --minFragPeaks 3 -w -v -i "D:\ms-data\waters\some-waters.raw\results_mgf\some-waters.raw"

You'll get an output like the following:

You can then convert this MGF with pwiz.