Could anyone please share their MS DIA methods or settings here?

[chingciripit]

Hi,

I am currently using Thermo Scientific Q Exactive mass spectrometer using ESI ion positive mode with a Phenomenex Kinetex 2.6 μm XB-C18 100 Å (150 × 4.6 mm) column. I can't seem to get meaningful data from my samples.

Thank you.

Ching

[michaelsteidel86]

• Are you refering to MS instrument method settings or DIA-NN parameters?
• Would you mind providing more details on sample type?
• Please share the a relevant log file.

[chingciripit]

I apologize for the confusion. What I meant was MS instrument method settings. My sample type is trypsin-digested bacterial cell lysate. log file attached p040_2.log.txt

Raw file: https://drive.google.com/file/d/1rhA4pHbPgDHBGQYCRmo7iCduKS5WPew0/view?usp=sharing

Speclib: https://drive.google.com/file/d/1YR_Mmlj47Y3kkqAMGeA3tbFDnDMeXRil/view?usp=sharing

[michaelsteidel86]

There various published ones, i.e. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7124470/ Optimal settings mainly depend on sample type and gradient length.

Would you mind sharing details on your MS settings?

[chingciripit]

Yes, please see attached. I was wondering if Q Exactive Orbitrap was suitable for DIA analysis? I can select the DIA analysis on the MS instrument settings. However, many papers that I've read seem to describe Orbitrap Exploris 480, not Q Exactive Orbitrap.

Thanks!

[michaelsteidel86]

Any further details on your MS/MS? How many windows, which mass range?

[chingciripit]

I believe such settings are not available on Orbitrap Q Exactive..