Thursday, August 23, 2012

What is in an MGF file?

Even if I'm the only person to ever reference this, I'm going to make a short series of this -- just to keep them straight.
We'll start with an easy one:  What information is contained in a Mascot Generic Format file (MGF) file?

Via Proteome Discoverer 1.3, I exported some Orbitrap Velos RAW data into every possible format.  The MGF file looks like this when opened in a spreadsheet

So, you get whether the mass is monoisotopic, or averaged, in this case - mono.
"BEGIN IONS" denotes that this is the place where Mascot should start paying attention, the Title line is a short statement that identifies this spectra.
 The first information is the parent ion mass. The next number is the parent peak area.  This is optional information that is not used in Mascot
The next line provides the charge state.  In our data, this was assigned within the Orbitrap when the isotopes were successfully resolved.
The retention time and the scan number are next, followed by the fragment ions and the area of their peaks (again, this is optional).  The last line is to tell Mascot to stop paying attention and to start looking for the next "Begin Ions" statement.


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  2. Well, been studying statistics for a while when teacher was teaching mgf, excited to see this is finally related with mass spect, but it turned out to be moment generating fuction!