I often do post-acquisition on mass spectra to increase mass accuracy for untargeted lipidomics or top-down proteomics studies. The procedure helped me with the Waters, Sciex, and Bruker mass spectrometers data. I have recently been working on data on a Thermo Orbitrap mass spectrometer, but I could not find a way to do post-acquisition mass calibration. Does anyone know how to do it? Thank you!
I should be able to use Excel to calibrate the peak list, but I hope to find a built-in method in Xcalibur or some other program.
To perform post-acquisition mass calibration on a Thermo Orbitrap mass spectrometer, utilize the EASY-IC™ feature for real-time internal calibration and consider using a specific calibration mixture for both polarities. Regular maintenance and checks are also essential to ensure accurate mass measurements.
Abdelhak Maghchiche Thank you for your comments! I do direct infusion, but calibrants often stay in the system for a long time and interfere with the spectra. Extensive cleaning is usually needed. I minimized the use of calibrants and instead used the peaks of known identity for pre- and/or post-acquisition calibration. It worked well for my previous experiments on Q-TOF instruments, and I would like to know if I could do the same on an Orbitrap mass spectrometer.
Abdelhak Maghchiche I tried EASY-IC for real-time internal calibration. It worked great for positive ion mode, but mass error was still significant for negative ion mode. Have you had any issues with negative ion mode internal calibration? Thanks!
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