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Topic: Mass tolerance and final alignment result (version 4.16) (Read 452 times) previous topic - next topic

Mass tolerance and final alignment result (version 4.16)

Dear users,

I recently processed my raw data (waters Q-Tof) using MS-DIAL 4.16. But I encounter some problems as follow,

1. My MS data exhibited a little large mass accuracy, I totally had 14 samples but the mass window should be +- 0.04da during all samples (1-2 sample had large mass variation).

2. So if I set the MS1 tolerance as 0.02 under mass accuracy in data collection of the MS-DIAL panel, some spike standards in these large mass variation samples have no peak height in the final alignment results list (please see the attached figure 1).

3. So I set MS1 tolerance as 0.035 and 0.05, respectively. It could find the correct peak height of these spike standards in the peak list including large mass variation samples. However, the spike standards mass features never be in the alignment results even I modified my alignment parameters (please see attached figure2 ).

4. I am not sure whether have other users encounter a similar issue ( spike standards in peak list but not appear in alignment list).

Please give me some suggestions or solutions in your available time.

Re: Mass tolerance and final alignment result (version 4.16)

Reply #1
Hi Bingpeng,

well, I have no experience actually.
In test-7 setting,
could you please try
1. accurate mass tolerance (MS1): 0.01
2. retention time tolerance (in alignment): 0.05 min
3. ms1 tolerance (in alignment): 0.055
4. N% detected in at least one group: 0



Re: Mass tolerance and final alignment result (version 4.16)

Reply #2
Hi Hiroshi,

Thank you for your suggestion and it does work. we could find the spike standards in the final alignments list.

But one more problem is the processing time. Now I total have six raw data but data process was very time-consuming.

My raw data was MSE data and from Waters MS machine. I remember the MSMS-abundance cut off should set a higher value to avoid a long time process. Now my parameter was set 500 as previously attached figure but also need 3-4 hours to finish total 6 data process.

So did u have any experience in this issue and could you reply to me in your available time?

Thanks in advance.