Converting text format Mass spectrometry data to mzXML?
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6.4 years ago

Hi friends,

I am having a set of ASCII format mass spectrometry (MS) data. I want to compare them to find out peaks with significantly different intensities. How can I do this? Are there tools for doing this if I had my data in mzXML format? If so then how can convert my data from ASCII to mzXML? I am attaching few lines of a file for your reference. Please help...

0,+,,ms1,-,line,100.7-3000.0,152,176.2 872016,909.2 910240,945.9 737760,963.6 710976,974.1 718016,...

0.028816,+,,ms1,-,line,100.7-3000.0,155,176.2 904904,834.0 712912,849.8 754160,889.7 752992,954.3 766272,...

0.0848331,+,,ms1,-,line,100.7-3000.0,159,176.2 949024,892.7 717104,958.5 741616,1110.5 1020704,1153.2 758320,...

mass spectrometry data formats mzXNL ASCII • 5.0k views
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You might need to choose a converter based on the original MS data source. A quick Google gives me these options: http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML#Converter_Overview

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Thanks Ram. But the problem is that I don't have access to the raw data. Any alternative?

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The solution is the most difficult of all - talk to people and try to figure out which corner of the universe the data is from. Or, read through samples of all formats and try to guess.

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It not that I don't know where the data is from. The data is from our own machine (Bruker). But the problem is I can't access the data right now. The question is precisely how can we write an mzXML file from a text data.

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Hmmm. In that case, you should be able to use awk to get each column's values (cols separated by ","), then nest them in appropriate tags if you know the structure of mzXML well.

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