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Working with Bruker DataAnalysis for data extraction and the TPP

Why is a Bruker DataAnalysis (DA) MGF file converter for the TPP. DA MGF file searched with Mascot or any other engine produces DB search result files incompatible with the TPP conversion to pepXML. However, DA is a powerful extraction software for file produced on Bruker intruments. This script offers users the possibility to extract their data in DA and analyse them in the TPP.

What is it doing? creates a new MGF file or DTAs directory that can be used for database search. DB result files can be then used in the TPP. In general, DA combines identical precursors into a single MS/MS spectra for database search. uses the mzXML file created with CompassXport to find scan numbers for each precursor and attributes to this single combined MS/MS spectra, the scan number that has the highest intensity. takes an MGF file as input and writes output to a new MGF file or a DTAs directory.

How is it working?

1. Extract data using DataAnalysis into MGF format

2. Create mzXML files directly from the DA export function or using CompassXport in command line

3. Copy or transfer all MGF files to be transformed into your TPP analysis folder

4. Copy or transfer all mzXML files belonging to each MGF file to the same directory

5. Convert using

Usage: (outputformat) (mode) mgffile


       -mgf Outputformat will be written in MGF format
       -dta Outputformat will be written in DTA format


       -s Keep a single MSMS spectra for identical precursors and attributes scan number by searching
          the precursor with the highest intensity in the corresponding mzXML
       -m Write the same MSMS spectra for each combined scan number done by Data Analysis

Ex: -mgf -s filename.mgf                     --> single file
       for i in *.mgf; do -mgf -s $i; done      --> multiple files

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