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mass tolerance

Just curious, why are the mass tolerance parameters in Da, rather than ppm?
The ppm difference between 100.000 and 100.001 is 10ppm, and between 300.000 and 300.001 it is 3.33ppm.
However, Agilent qTofs are only able to reach 10-15ppm mass accuracy when acquiring samples in matrix (eg, plasma/urine). A setting of 0.001 Da would be too narrow for 300m/z. I would need 0.003 Da for 10ppm. But, using 0.003 Da for 100m/z would be 30ppm, which is too large.
Perhaps I'm thinking about this incorrectly?
For metabolites such as organic acids, a qtof with a resolution of 10,000 at 120m/z, and 10ppm mass accuracy, what tolerances do I use?


Re: mass tolerance

Reply #1
Please see below for the description of the current MS-DIAL program.

(1) the user-defined mass error (e.g. 0.01 Da for MS1 tolerance) is converted to "PPM" unit considering 500 Da as the target mass.
(2) if the mass is greater than 500, the mass tolerance is newly calculated as follows (see below).

User defined tolerance   0.01 Da
Converted to ppm: 20@m/z 500

m/z   tolerance
500   0.01
600   0.012
700   0.014
800   0.016
900   0.018
1000   0.02
1100   0.022
1200   0.024
1300   0.026
1400   0.028
1500   0.03
1600   0.032
1700   0.034
1800   0.036
1900   0.038
2000   0.04

(3) the converted mass tolerance is used for (1) the MS/MS spectral assignment to precursor ion and for (2) the m/z filter in searching spectral libraries for compound annotation.
*Note that the mass tolerance for <500 Da is not converted accordingly in the current program. It means that the mass tolearnce is set to 0.01 Da for <500 Da metabolites in spectral searching.