ms1 and ms2 tolerance

[wangss3]

Hi,

1. I have a sciex qtof 7600 and orbitrap HF. How can I know the optimal ms1 and ms2 tolerance. For qtof every time set as 0? 10ppm or 15ppm for Orbitrap?

2. Is there any function like DIA-NN's pipeline in window GUI? I have to run first and second search manualy every time?

Best, Ko

[wangss3]

Use this optimized parameter for all future search?

PROGRESS: Search parameter optimization finished. Values taken forward for search are: 2:50:50.152362 PROGRESS: ============================================== 2:50:50.152362 PROGRESS: ms2_error : 5.3499 2:50:50.152362 PROGRESS: rt_error : 1024.5078 2:50:50.162362 PROGRESS: ms1_error : 9.2534 2:50:50.162362 PROGRESS: ==============================================

[GeorgWa]

Hi,

if you don't know, search a triplicate with MS2=0 and MS1=0. Then have a look at the stat.tsv table where the optimal value is reported. You can also use the tolerance which was reported by DIA-NN.

To give you some intuition: For ScieX 7600 I usually use 15ppm MS1 and MS2. For the Orbitrap it depends on the transient. I would use 15-20ppm with 30k resolution, 10ppm for 60k resolution, 5ppm for 120k resolution (mostly MS1)

Leave RT optimization always on (RT=0).

I hope this helps, Georg