lgatto
commented
2 years ago It does indeed look like you have a peak of similar m/z co-eluting with beta-carotene. Note that your question is probably not a good fit for here, as I can't see any link with MSnbase.
Closing for now.
Hi,
I have a general question regarding quantitation of molecules from HPLC-tandemMS using MS1. I know this is not up to a chemist's standard, but as a biologist I just want to see if there is a general trend between the data and other variables i am measuring. I am very grateful for any reply or input, thanks!
Lets say i have 10min retention time and 10 samples (plus the standard, biological blanks and instrument blanks) and i extract the spectrum from each sample at the appropriate retention time based on the standard. lets say this was at exactly 5 min. I subset the mz axis of this spectrum for my molecule of interest, beta-carotene, which from the standard gets a mz of 537.440918.
My plan was then to calculate the area under the curve from 357.3 to 357.5 (see matrix below). However, all my samples, including my blanks and the standard, all have a considerable peak at 537.49 - I do not know what this is...
Is this just very unfortunate for me? Does anyone have any tips? My interpretation is that I will not be able to quantify beta-carotene because of this unknown molecule which is overshadowing my molecule of interest...
Can I try just selecting the line where mz== 537.4409 and use the intensity value only, rather than area under curve calculation?
example from blank sample: $KK_20210457_APCI_POS_Blank4.mzML mz intensity rt 36168 537.3499 0 6.6164 36169 537.3600 5 6.6164 36170 537.3701 16 6.6164 36171 537.3802 9 6.6164 36172 537.3904 12 6.6164 36173 537.4005 0 6.6164 36174 537.4106 8 6.6164 36175 537.4207 26 6.6164 36176 537.4308 55 6.6164 36177 537.4409 181 6.6164 <-- this is the mass of my molecule of interest 36178 537.4510 249 6.6164 36179 537.4612 450 6.6164 36180 537.4713 1031 6.6164 36181 537.4814 1572 6.6164 36182 537.4915 1889 6.6164 <--- something else (also in blanks and unrelated purified standards) 36183 537.5016 1391 6.6164 36184 537.5118 480 6.6164 36185 537.5219 188 6.6164 36186 537.5320 161 6.6164
Thank you so much for having a look at this! Lasse