Average mass of carbon in GPMAW
The average mass of carbon is defined by IUPAC as 12.011 with a natural distribution of 12.0096 to 12.0116.
This value was originally used by GPMAW, but as high mass instruments are becoming more and more precise, a more accurate value has been needed. The average mass of carbon has thus been revised to 12.0107, a value that seems to be generally agreed upon. This value has for some years been the default value used in GPMAW.
However, as upgrading a GPMAW installation does not overwrite user-accessible files (among these the standard GPMAW.MSS file), some users may be left with the old value of 12.011. Although the difference of 0.0003 Da is slight, when calculating the mass of an IgG heavy chain contains 2200 carbon atoms, this amount to .66 Da and close to 2 Da for an intact IgG.
What to do:
If you calibrate your mass spectrometer using proteins for which the mass has been calculated by GPMAW you should be alright. However, if you use standards calculated by others (e.g. the instrument maker) you have to check which carbon mass value was used.
In GPMAW you select Edit | Edit mass table (or press Ctrl+Alt+A) and you will get the atom molecular weight table: