Not able to find a way to convert the file for having all the MS MS spectra in a text file.
Try exporting to .csv file format initially. (Check whether you have this facility in your system). From .csv file format you can convert the data to a .txt format in an excel spread sheet.
I have used this when trying to convert the raw chromatograph data to txt format, which worked out well.
Hope this works for your application as well
Sridhar, AB SCIEX offer a tool called MS Data Converter, free download at http://www.absciex.com/downloads/software-downloads. It converts to mzML1.0 and mgf. mgf is actually close to a txt type representation of all MS/MS spectra after centroiding. With some editing, you might be able to use it for Massbank or similar.
I exported to mzxml using the software proteowizard (msconvert) because I was having problems with command line prompt of the msconverter. However I see that mzxml files are huge ~ 600 mb instead of the 30-100 mb .wiff files. The text files I previously used in Waters data used to be very small (~ 1mb). Does even the mgf file have the same size, as I need to send this data to someone.
wiff is actually a compressed format, like a zip file. mzML and mzXML contain only slightly reduced data, but without the compression, so are usually huge files. mgf is actually much reduced, it is only a centroided x/y lisiting of all fragment ions in all fragment ion spectra. In our hands a 500 MB wiff can easily produce a 500 MB mzML, but usually only a 20-30 MB mgf, so mgf is way more portable.
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