Incorrect precursor m/z when loading MGF file from GNPS

[liannette]

When loading the MGF file into Spectrum object, the m/z of the precursor ion is imported/calculated incorrectly.

In the MGF file, the "pepmass" of a spectrum/feature is given. Currently, this pepmass is divided by the ion charge to calculate the precursor m/z.

However, this step is unnecessary. The pepmass value is equivalent to the precursor m/z value, they are just two different terms for the same thing - the m/z of the ion selected for fragmentation.

[liannette]

@CunliangGeng I don't think that I can assign this issue to myself, can you do it?

[justinjjvanderhooft]

@liannette I did it....

[CunliangGeng]

However, this step is unnecessary. The pepmass value is equivalent to the precursor m/z value, they are just two different terms for the same thing - the m/z of the ion selected for fragmentation.

From the https://www.matrixscience.com/help/data_file_help.html#GEN, what I got is that PEPMASS is peptide mass but not m/z. They may have same values but we should treat them separately in the code. Are you sure we should use pepmass for m/z? If so, you have to give your comments in the code to make it clear.