Hello everyone! I recently had an LC/MS analysis (not MS/MS, as the operator doubled the price) done for the extract of my plant sample. I plan to include these results in my manuscript. To support this, I’ve found a couple of papers that report LC/MS/MS data for other species in the same genus (my species is Limonium otolepis, while the others studied include Limonium gmelinii, etc.).
I'm currently preparing a table that lists the observed and calculated mass values. When an observed mass in my data is nearly identical to one reported in another Limonium species, I mark it as also being present in L. otolepis. However, many of the observed mass values in my results differ from both the calculated masses and those reported in other species.
I also noticed that in the papers I reviewed, there were some discrepancies in mass values, or the exact observed masses were not shown. Instead, the compounds were identified based on their fragmentation patterns.
My question is: What should I do in my case? Is it acceptable to report the observed mass values and make tentative identifications based on similarities and small differences, or is further analysis (e.g., MS/MS or fragmentation pattern studies) necessary? If I submit my manuscript without fragmentation data but with other sections like antibacterial test, isolation procedure of a compound, will my manuscript accepted? Thank you for your answers, I'm attaching a table and a TIC with a mass spectrum
First, to answer You question, You should definitely consider repeating the measurements, preferably with MS/MS. I don't want to throw any accusations, but to me it looks like the MS operator did a bit sloppy job here and the spectrometer was not properly calibrated (if this was measured on a Q-ToF machine this is quite plausible... You can see that mass errors are kind of similar in each case). What I did when measuring on Q-ToFs was to add calibration segment at the beggining of each LC run - whis way You could always check if masses are ok and recalibrate in software if neccessary.
Still, for reporting something in publication I would go with golden standard - max 10 ppm mass difference (even lower on more accurate mass specs, I preferred 5 ppm). Also to confirm anything You should have results from two methods - for a long time now results from MS and MS/MS were treated as such, so measuring MS/MS is in fact a good practice... unless You have some other results (e.g. NMR) to confirm.
Dear Paweł Pasikowski ! Thank you so much for your answer. The instrument was CHIP-Q-TOF Agilent Technologies 6520B as the operator mentioned in a methodology. Regarding the calibration, he did not mention anything. ppms are too high, in all cases above 100 ppm. I understood that I must have MS/MS results. I don't know what the next is, It is the only place in my country (Uzbekistan) where they do this type of analysis.
Yeah, I feel Your pain. There are more places to do commercial LC-MS analyses in Poland, but You would be surprised how crappy results one can sometimes get from such measurements. You can always consider doing this somewhere abroad, but I assume that prices will be higher and sample shipment adds to the price. Maybe You can try to go back to the lab that did this analysis and politely ask them to repeat due to bad calibration and additionally pay them only for adding MS/MS? (but You should be careful here, as You do not have any hard evidence, that this is the case... still, this is the most plausible option IMHO).
Good luck!
Well, I agree with the Paweł opinion. It looks like a systematic QTOF tuning error. Be aware that MS/MS analysis will not always give you more information. In particular, some organic acids tend to produce only acetate anion during fragmentation in negative mode. IMHO the accurate mass measurement is a must in this case.
Dear Andrzej Wasik Thank you so much for your reply! Now I understand that the operator should think about calibration of the instrument using the known compounds
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