Dear users,
I recently encountered a problem, some of the features in alignment results appeared a lot of zero values but the features could detect well in MS raw data (please see the attached file). Here we take a DAG (18:1/18:1) as an example, the mass of DAG (18:1/18:1) could be observed in all 6 replicated data but in final alignment list, M-1 and M-5 peak height changed obviously compared with other four data. From MS-Dial, it seemed to mislabel it as isotope (M+1) in M-1 and M-5.
So could anyone tell me what's the reason and how to correct it by setting the proper MS-DIAL parameters?
Thank you very much.
Best,
Bingpeng
Sorry for forgetting upload the parameters of MS-DIAL. Please see the attached figure for parameters detail.
Best,
Bingpeng
Hi Bingpeng,
sorry for the late reply.
Could you please let me know all the parameters of MS-DIAL? Otherwise, I cannot make a suitable suggestion for you...
Maybe, it can be resolved by changing the parameters of alignment tab.
Did you tick the checkbox of "gap filling by compulsion"?
Hiroshi
Hi Hiroshi,
Attached please find the capture of all parameters.
In addition, I didn't tick the checkbox of "gap filling by compulsion".
Please give me your suggestion, thank you very much.
Best,
Bingpeng
Hi Bingpeng,
just try to tick the option of "gap filling by compulsion", please?
Hiroshi
Hello! Has this issue been resolved? I think I am seeing similar things with my data where when I did manual data analysis of the raw data and I saw the peaks there with good %CV's with the replicates but bad CV's when running it under MS-Dial. Thanks.
Hello, the issue wasn't resolved and I already used the data for further analysis. Fortunately, only fewer features were observed similar issues. I also tick the option of "gap-filling by compulsion", but it still has zero value.
Thank you for your response. I will probably post a new one for my dilemma and see if others can help me. Have a good evening and keep safe!