Different machines generate raw data in different formats. A typical first step is to convert your specific raw data into a commonly used generic format like mzXML or mzML.
You might then want to convert this into other formats for downstream analysis. E.g. you might convert into MGF to allow the software Mascot to identify peptides in your data.
So your first step should be to identify the machine your data comes from. I strongly suggest you go back to the person who gave you the data and request more details about the experiment - without knowing exactly what you're looking it, it will be very difficult to perform a meaningful analysis (e.g. different software is optimised for different machines). Also, you should know things like whether labeling like SILAC was used.
If for some reason you can't do this, perhaps you can post some examples of the filenames/directory names you have, and somebody here might be able to recognise the machine. For example, Agilent raw data is stored in ".d" directories.
The following website provides a large list of mass spectrometry software, including format conversion utilities:
See especially msconvert, which converts "from RAW / WIFF / T2D / Agilent / Bruker / Waters / mzML / mzXML / MGF / MS2 to mzML / mzXML / MGF / MS2".
modified 7.8 years ago
7.8 years ago by
Bio_X2Y • 3.6k