In a current study, I have utilized the UPLC-MS-MS to identify the phytochemical components of a plant extract. Using the aid of a database, a group of phytochemicals was suggested to exist. In the process of verification of these compounds, I applied the mass error (in ppm) for the molecular ion peaks obtained by the equation (observed mass-theoretical mass/theoretical mass *10^6), and I made sure that the mass error did not exceed ±10 ppm. Here is my question: Is it a must to apply this equation to every fragment, or is it enough to make sure that the observed mass for the fragments does not exceed ±5 ppm of the theoretical mass?
Hi,
What type of mass spectrometer did you use to acquire your data? Did you perform high resolution MS and MS/MS?
Usually, MS/MS is performed with lower resolution acquisition as compared to the acquisition of MS data: in that case, the mass error of the parent mass should be low. The fragments confirm the identity/structure of your analyte, complementing the elemental composition suggested by the accurate mass.
Hope this helps.
Thank you; it helps a lot.
I utilized XEVO G3 QTof mass spectrometer with high-resolution MS
In LC-MS/MS, it is best practice to apply mass error calculations for both the molecular ion and fragment ions, with typically tighter ppm tolerances for fragments to ensure confident identification. Verifying that mass errors for fragments do not exceed ±5 ppm alongside molecular ion checks strengthens compound verification accuracy.
Thanks a lot for your illuminating answers
Abdelhak Maghchiche, a final question, mass error calculations means (observed mass-theoretical mass/theoretical mass *10^6), not (observed mass-theoretical mass), is it right ???
Mass error in LC-MS/MS should be calculated for both molecular and fragment ions using the formula (observed mass - theoretical mass) / theoretical mass .106 ppm, with tighter tolerances for fragments, usually ±5 ppm, to ensure accurate compound identification.
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