mass tolerance

mass tolerance zhengemma  2017-03-29
Can the method match tolerance be set above 0.6 under the Transition settings? Is there a way to do?

Brendan MacLean responded:  2017-03-30
Hi Yuzi,
Can you explain why you would want to do this? I extended it up to 0.6 from 0.5 on a specific request from a researcher who is no longer in the field, and I now feel that even going that high is more likely to just cause you problems than allow you to do anything useful. I think you should be very much questioning what you are doing in going about a method match tolerance of 0.1.

Please explain further, and I will see if I can help.

kbagramyan responded:  2019-12-17
Hi Brendan,

I am glad that I found the question that I wanted to ask you too. We recently performed an MRM analysis using 6495 LC-MS Triple Quadrupole (Agilent). We optimized the MRM transitions for the quadruply charged precursor ions of the light and the heavy peptides. Here, are our transition settings used in the method: 545.3 (precursor, +4) and the transitions are 509.0 (b, 4+); 640.0 (b, 3+); 678.3 (b, 3+). The Skyline recognized the two of transitions such as 508.5155 and 639.67. The third transition of 678.3 in our method was 677.6849 in Skyline transitions giving 0.6151 Da difference. Unfortunately, this was the most intense peak but wasn't accepted by Skyline because I couldn't extend the method match tolerance above 0.6.

The data look very good and I was wondering if there is a way to extend the method match tolerance, so I can include that transition for accurate quantification?

I hope I was clear and was able to describe the problem.
Thank you in advance,

Karine Bagramyan, PhD