Check whether the quadrupole resolution is in line with your calibration. Your
PPG calibrant is singly charged and you are measuring an exact mass whereas the
myoglobin peaks are 10- to 20-charged and you are measuring an average mass. If
the resolution of your quadrupole is not carefully controlled (i.e. if your
quadrupole only achieves 900 resolution instead of a 1000), the mass measurement
will be less accurate for myoglobin (it will drift by a couple of 100 milidalton
at the full mass spectum level, resulting in a drift of a couple of Da when you
deconvolute) while it be still OK for PPG. On my instrument, I always use
separate calibration files for proteins and peptides exactly for that reason.
Mass measurements are then considerably more accurate.
Hope that it helps.
Axel
-- --------------------------------------------------------------------------------Axel Ducret, Ph.D. Senior Research Biologist Merck-Frosst Canada Inc. Dept. Biochemistry and Molecular Biology P.O. Box 1005 Pointe-Claire-Dorval PQ H9R 4P8 Canada
tel. + (514) 428-3428 fax + (514) 428-4900