What mass tolerance should I use to detect the PTMScan® Control Peptides?

We recommend users to use the appropriate mass tolerance window based on historical performance of their LCMS instrument, the settings of the acquisition method and elapsed time from their most recent mass calibration.  For instance, when we acquire our data on a Q-Exactive with lock-mass activated, we generally use a tolerance window of 2.5ppm for the extracted ion chromatograms of the Control Peptides.  Generally, a window of up to 5ppm should be appropriate for most users operating an Orbitrap based instrument that is recently calibrated (i.e. within a week).  For Ion-Trap based instruments, users may need to use a higher mass tolerance window.
 

Last updated: September 12, 2024