I am working on an undergraduate bioinformatics project but I have reached an impass in my workflow.
I am trying to convert a .wiff file from a TripleTOF 5600 instrument to MGF format using msconvert.
The input file is ~2.7 GB and the resulting MGF file is ~29 GB and is seemingly random data.
The output looks something like this:
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Each peak list has hundreds of peaks at very small m/z increments from 114 on up with intensities of only 0.0 and 10.0
I would expect that the MGF output would be much smaller than the .wiff input as well so obviously there is something wrong. Has anyone else ever encountered this problem?
the .wiff file is from this data repository on PRIDE
the specific files I was using are Duo_CTRL_200ng_BSA1fmol_SWATH_20121003_01.wiff and the corresponding wiff.scan file
Any help would be much appreciated