The visual inspection of MS/MS spectra is a preferred way to refine and inspect some of the unknown tandem mass spectra. The freely available NIST MS Search GUI is the gold standard for visual MS/MS search and comparison. It can read the common MGF, MSP and JDX and many more formats. It is not recommended to load more than 10,000 MS/MS spectra because of the 32-bit nature and memory limit of 2 Gbyte of the program. For such purposes see MS/MS batch search. However the NIST MS Search GUI uses libraries that can hold many hundred thousand spectra without a problem. Make sure the LipidBlast libraries are properly included in the search settings and precursor and product ion window are correctly set. Also important is to activate MS/MS search in the search settings.

LINKS and downloads

  • NIST MS Search [LINK]

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