I'm looking for an open source program to open a ".dat" file.
The file is the result of a MASCOT search performed using peptide MS/MS data.
Unfortunately, I did not manage to find any suitable program so far, do you have any suggestions?
You could have a look at our mascotdatfile library for Java ! It's found at https://code.google.com/p/mascotdatfile/wiki/Introduction
A .dat file is just a text file and it can be opened with any sort of text-editor. If you have windows, I would recommend using notepad++ or kate if you have ubuntu.
However, if you want to actually process the .dat file and get useful information out
e.g. the Mascot Ion Scores, expectation values etc you could either use a library like that suggested by Kenneth or the library made by the Mascot guys themselves.
An alternative that I would recommend because it's friendlier is to convert it into pepXML e.g. with Mascot2XML in TPP.
Hello,
thank you very much for your great hint!
I tried both method (mascotdatfile also before posting the question).
Concerning mascotdatfile I just cannot open the executable jar file. It simply does not start.
Then I tried to install TPP to use Mascot2XML, and also here I have some problems. The point is that it simply does not connect to the localhost via Apache at the start. I tried to consult the FAQ section and different forums but with no success.
I would like to open my .dat file to access the MS/MS scan, which the I would like to submit to PRIDE.
Thank you again for your help.
I wish you a great a successful 2014.
Best
Stefano
Hey Stefano,
So you're trying to map a Mascot query e.g. q1_p1 to the corresponding ms/ms that it was derived from? If so, you'll need to be a little careful because the query order doesn't equate to the ms/ms scan.
Also, if you wanted the peak lists of the ms/ms then my suggestion of converting to pepXML wouldn't work as these files don't retain the peak list.
Keep in mind it's a library, not an executable jar ;) You'll need some java-coding...If you'd want more help on the topic, let me know :)
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