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PNNL-Comp-Mass-Spec / LIQUID

Software tool for identifying lipids in LC-MS/MS-based lipidomics data
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Unit and window for HCD mass error #2

Open tobigithub opened 7 years ago

tobigithub commented 7 years ago

a) There is an HCD and CID mass error, but no unit is given in the GUI. Also one is 50 and the other 500 by default? Would it be possible to insert the unit [ ppm, Da ] and focus [precursor, product ion] into the GUI?

b) Also is the "mass error" meant for the precursor ion and/or the product ions?

c) Plus in the result list there are errors that are 2000 ppm, which does not really make sense, especially if a mass error range is required?

Exact m/z   Formula         Observed m/z    ppm Error
988.833        C64H110N1O6  991.5167926 2706.452028
988.833        C64H110N1O6  991.5167926 2706.452028
990.849        C64H112N1O6  991.5225446 679.3033678
990.849        C64H112N1O6  991.5225446 679.3033678
GrantFujimoto commented 7 years ago

A) 1 - The boxes represent ppm tolerances. I will add labels to them to make that clear. 2 - I am unsure what you mean by focusing the precursor or product ions in the GUI. Can you please elaborate?

B) Mass error is meant for the precursor ion only.

C) We have never seen any ppm errors even close to that large. Can you please send us the raw dataset for us to look into?

tobigithub commented 7 years ago

a1) OK. a2) the precursor window is filtering all precursors, additionally the product ion tolerance can be set
to allow for product ion filtering. Its a feature of the NIST MS Search program. https://www.nist.gov/sites/default/files/documents/srd/NIST1aVer22Man.pdf

B) OK.

C) I think the error is not data set related, because the filter should take care of filtering allowing only a certain ppm range, lets say 10 ppm. However I can share those files for sure.

Thank you!