Subtracting in SIM mode for data analysis

Discussions about GC-MS, LC-MS, LC-FTIR, and other "coupled" analytical techniques.

8 posts Page 1 of 1
hi every one
my issue about subtracting in interpret data .
when i analyse biological sample like urine search about morphine ,
i use SIM mode method and inject 1 microm. but the peak is very small but no noise still a peak .when i search by ions the library start to read morphine but low match .when i make subtraction the percent will elevate ..
question is ,can i make subtraction for peak in SIM mode .or only done in scan mode ..
thanks every one
Doing a library search with SIM data will not result in a match that makes sense or is defensible. Unless you had 20 or so major ions in your SIM acquisition, in which case you are not benefiting by doing SIM at all (assuming you are using single quadrupole MS). SIM should only be used when you KNOW your chemical elutes at a specified RT and you are fairly certain you won't have any background contribution to your quant or qualifier ions in a given matrix or prep method. In Low Resolution MS, SIM is used to enhance the signal of selected ions only. If done properly, background subtraction should not be needed for adequate quantitation, and a library search will be meaningless because you will not have enough ions to reproduce a spectrum for search.

My suggestions is that if your goal is purely "qualitative" and you don't want to know how much chemical there is then switch to Full Scan and do a library search after subtracting out the time in front of the peak.
~Ty~
tlahren wrote:
Doing a library search with SIM data will not result in a match that makes sense or is defensible. Unless you had 20 or so major ions in your SIM acquisition, in which case you are not benefiting by doing SIM at all (assuming you are using single quadrupole MS). SIM should only be used when you KNOW your chemical elutes at a specified RT and you are fairly certain you won't have any background contribution to your quant or qualifier ions in a given matrix or prep method. In Low Resolution MS, SIM is used to enhance the signal of selected ions only. If done properly, background subtraction should not be needed for adequate quantitation, and a library search will be meaningless because you will not have enough ions to reproduce a spectrum for search.

My suggestions is that if your goal is purely "qualitative" and you don't want to know how much chemical there is then switch to Full Scan and do a library search after subtracting out the time in front of the peak.


many thanks prof."tlahren for your replay ..
Yes i know the eluted chemicals ,and i know its RT .
my job about analysis of biological samples like urine, blood and viscera in forensic lab.i do scan mode for many cases ,but in other which give positive morphine or tetrahydrocannabinol in immuonoassy .i take these samples and make confirmation by elute in GC MASS AFTER HYDROLYSES..
my problem is about SIM mode ,as when i elute morphine with BSTFA .some cases give peak in exact RT .library read morphine TMS with match 90%.OR ABOVE
other give v,small peak whith match 65%.and i do subtract to these peak .give high match become 85%or Less ..my question .is these true (do abstraction in SIM mode 0.
or SUBTRACTION ONLY DONE ON PEAK SCAN MODE --
these is big problem we face in our lab as cases read 60% we consider it negative .when matching equal 85% or above we consider it positive ..
so by subtraction the sample become positive ..
and we deal with addicted person as we belong to ministry of justice---
..
sorry for these details and wast your time .but these is an important issue we face ,we need your help
many rhanks
Have you tried to do the confirmation using LC/UV or maybe LC/MS so you don't need to do the hydrolysis? You may be able to achieve lower detection limits the LC because you can inject a larger volume of the sample. The two analytes you mention give good chromatography with LC when in native forms.
The past is there to guide us into the future, not to dwell in.
Agreed that, in a broader sense, you shouldn't be using SIM to search libraries for qualitative identification.

SIM essentially accomplishes two things-it reduces noise by being invisible to many of the common background contaminants, and increases the amount of time that a target m/z is allowed to pass through the quads(full time in the case of single SIM, and when monitoring multiple ions each selected m/z spends more time able to be filtered out by the quad) .

You can see easily see the effect on noise if you take a full scan and then use the extract ion function(not sure what manufacturers other than HP/Agilent call it-I'm still looking for it in Varian MS Workstation!). When I was in graduate school, I spent a lot of time quantifying the same three analytes. There was a fourth one we expected to be present but if what I'd seen/proposed was correct it should have been in there in trace quantities. It was "lost" in the full scan spectrum, but I was able to distinctly see it in an ion extraction. In retrospect, once I'd identified the three major peaks(which initially were a complete surprise to us) I should have used SIM because in all cases everything was there at low concentrations anyway and I could have had "cleaner" quantitation, but that has long passed.

If you see a chromatographic peak representing the major m/z at the expected RT, that is as close as you can get to a definitive identification. Because a SIM spectrum will represent a single or a couple of m/z values, library searches WILL NOT match except in very limited cases where the base peak represents the vast majority-either from lack of fragmentation or from mostly giving one large fragment. Caffeine is often one of my go-to GC-MS system check standards for this largely because I've spent enough time that I can usually make a good guess at RT in the instruments/columns I use regularly and because its base peak in full scan is a very, very large m/z 194(that I can't get to fragment appreciably even in a triple quad). It will usually library match on SIM at 194, but it's one exception I can think of.

When doing SIM, integrate as you would for full scan and as long as you've done your standards in SIM also, you will get perfectly good quantitation(in fact probably more reliable than full scan, although that's going to be sample specific).

That brings up a broader issue to me, though, given that you're working in a forsensic laboratory. The entirety of my experience is in academic labs, where all of our instruments(including GC-MSs, which are my pet instruments) serve an entire department need to be able to handle a wide variety of samples with different specific needs. With the caveat that I've never worked in a forensics lab, I would expect there to be established if not published protocols for any analyte that you need to either ID or quantitate. If not, and you're basically trying to make the instrument give a certain result, in my mind that opens up a huge hole in any results you are delivering and I would question if they could(or even should) hold up in the legal system. When I do look for things like drugs(or drug metabolites) I always stress that my results are for interest only and carry not guarantee. I usually follow literature-published methods, but often tweak them for my specific instruments or even when I see opportunities to improve LODs. Rarely does anyone other than me even look at my results, and if they do it's in a vague yes or no presence that I won't even put on paper because I don't want anyone using that for other purposes.
I don't know about the newer units but the Agilent 5973 MS can use a fast scan card to do simultaneous SIM/Scan. You get most of the detection limit benefit of SIM but you also get scan results.
LALman wrote:
I don't know about the newer units but the Agilent 5973 MS can use a fast scan card to do simultaneous SIM/Scan. You get most of the detection limit benefit of SIM but you also get scan results.


All of the 5975 and up can do it ( except the 7000QQQ with older software, it is enabled on the newer software though)

The 5973 requires the Fast Scan electronics which are either an upgrade or on the last models sold. The early 5973s can't do it simultaneously.
The past is there to guide us into the future, not to dwell in.
I am not certain whether a spectral match from a weak, subtracted spectrum is any better proof than a good match from well-chosen qualifier ions whose peak areas have been assessed with decent precision as SIM ions.
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