Chromatography Forum

Hi

I would greatly appreciate any suggestions regarding those questions:
I have a read a publication which says that the acquisition mode of MS was TIC (50-550 amu) but identification was done using m/z 99 fragmentograms. Does that mean that after TIC, the authors run SIM or fragmentograms refer to extracted ion profiling? 

The majority of publications on analysis of alkanes by GC-MS uses TIC rather than SIM. Is there any reason for that? Alkanes give characteristic fragment ions that could increase the sensitivity of analysis therefore I wonder why they choose TIC.

Thanks again for your help.

Why not both. Do simultaneous SIM and Scan. SIM gives you sensitivity and Scan gives you better identification information (assuing you have enough present for a library search on scan).

You're right, doing TIC and SIM would be the best option. Thank you for your reply.

Does anybody have an idea regarding 'fragmentogram'? I can't find the definition of this word but it usually appears within the context of one m/z therefore I'm guessing it could have something to do with EIP (with SIM we would use at least 2 m/z).

Hello

Just remember that SIM sensitivity in SCAN/SIM mode is lower that only SIM run.

Regards

Tomasz Kubowicz

Thank you, Tomasz.

Does anybody know if mass chromatogram as defined by Schimdzu:
http://www.shimadzu.com/an/mc.html

is the same thing as extracted ion profile? It is for one specific m/z, however in EIP usually more m/z are selected (I think...). However, both are still acquired in TIC, aren't they?

I'm pretty sure that's what they are doing. They're just sorting the TIC by a specific mass to make everything else disappear. I've never heard anyone use the term "fragmentograms" in all the years (more than 25) I've been working with GCMS.

Hello

In all softwares you have option "extract ion/ions" from TIC. I believe that what they do.
Is it SIM - No. In my opinion it is another tool for sales people to impress customers

Regards

Tomasz Kubowicz

... However, both are still acquired in TIC, aren't they?

Not exactly. Aquired in SCAN mode. TIC is different term.

Hello

Thank you for all your help, it's much clearer now.

dblux_, you're right, the acquisition mode is scan (or total scan), which results in TIC. At least that's what I've always been taught.

Following the "Next" link on the Shimadzu tutorial page to which amateur23 posted a link will take you to Shimadzu's description of SIM, which clarifies the way in which it differs from an extracted mass chromatogram.

Extracted mass chromatograms, taken from TIC data, are far more than a sales tool. If you know exactly what you are looking for, you will collect SIM data (assuming you're using a quadrupole instrument) because it's far more sensitive. If you don't know what you're looking for, you will collect scan data. If you then find an interesting ion in the scan data from a complex sample, you'd be insane to integrate the TIC because it might contain hundreds of peaks, mostly coeluting. Instead naturally you will extract a chromatogram of the appropriate mass, which will probably contain only a handful of peaks, and integrate this.
No, it's not as sensitive as SIM, but you can't set up a SIM experiment when you don't know what you're looking for.

This, incidentally, has always been Thermo's argument when selling high-resolution instruments in competition with triple quads: if you're looking for drugs of abuse, MRMs in a triple quad can only look for drugs you know about. If someone comes up with a new drug, you can mine accurate mass data retrospectively. So if you can get your specificity by accurate mass rather than MS^2, your data-set is more useful. I don't completely agree, because MRMs can potentially distinguish isomers, which accurate mass cannot. But Thermo have a point.