Recommended ppm setting for an Orbitrap Exploris 240

[Benjamin Parker]

Hi, 

What is the recommended PPM setting for a Thermo Orbitrap Exploris 240?

Best

[David Tabb]

Hi, Benjamin.  Did anybody reply yet?

In the past, when I've used Comet with Orbi hi-res MS/MS scans, I've used an MS/MS m/z bin size of 0.02.  This corresponds to something Jimmy published: " In fact, the optimum mass bin width is 1.0005 for low resolution data such as that acquired on an ion trap detector, and we recommend a mass bin width of 0.02 for high resolution spectra." (https://doi.org/10.1007/s13361-015-1179-x)

If you're asking about a precursor mass tolerance denominated in ppm, most well-calibrated Orbi data can be searched with 10ppm or 20ppm tolerance.  I have on a couple of occasions dealt with data from an Orbi WAY out of calibration, where the ppm tolerance exceeded 20ppm.  In a case like that, the proper answer in an ideal world is "run maintenance on your instrument and recollect the data!"

Good luck!

Dave

[Benjamin Parker]

Hi, Dave,

Thanks for the message. Nobody else has replied. 

I'll try the settings you recommended. I've noticed that working with my samples (I'm doing crosslinking-MS on a single purified protein) need to use different settings for our QTOF vs our Orbitrap. 

Ben

[David Tabb]

When I first started working with QTOF data (around the time of the QSTAR Elite), I assumed that their mass accuracies would be more like 50ppm than the 10ppm I enjoyed on the Orbitrap.  These days, though, I usually assume the same degree of mass accuracy will result from a timsTOF or TripleTOF as we get from an Orbitrap.

Cross-linking is a really challenging area for data analysis.  I wish you good luck!

Dave

[Jimmy Eng]

Benjamin,

Sorry for not responding earlier and I'm grateful that Dave chimed in.  I don't know why but I simply don't get notified of some posts to this Google group so I'm not aware of them until I visit this group to post something.  If there are any open questions still please follow-up.

Jimmy