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Topic: The use of RI for Alignment and Identification (Read 90 times) previous topic - next topic

The use of RI for Alignment and Identification

Dear appreaciated Forum,

Our instrument has a stable performance and the retention does not shift dramatically (~4 seconds in 250 runs). We had just a few samples which contained alkanes for setting up an alkane dictionary. Here the alkane mix was added to the sample after the first GC Injection to avoid co elution. Most of our samples do not contain alkanes. In conclusion we consider the RT as an effective alignment parameter which I want to use for the alignment (which I have discussed here: http://www.metabolomics-forum.com/index.php?topic=1570.0).

But:

MS Dial seems to expect the presence of alkanes from the dictionary in each sample, right? So far I haven't received reliable RI values for samples that do not contain the alkanes themselves. (I took the Retention Time of the alkane dictionary from an representative sample of the same sequence).



For identification purposes the RI is an important parameter. But do I really need alkanes in each sample if there was no severe shift in the retention time? In my oppinion libraries have greater variation in RI (due to differences chromatography) than samples from one sequence. So there is no need to have a very precise RI estimate for each peak when comparing this to a highly variable RI from the library.


I looking forward to your comments. Do you always add alkanes to all samples? Do you prepare an alkane dictionary for each sample individually (since there are always RT differences in the alkane peaks among two samples) or how does MS Dial detects the alkane peaks in each sample?

Kind Regards,
Stefan

Re: The use of RI for Alignment and Identification

Reply #1
This can be deleted, I clicked on the wrong button  :o

Re: The use of RI for Alignment and Identification

Reply #2
Dear Stefan

...anyway...
>>MS Dial seems to expect the presence of alkanes from the dictionary in each sample, right?
Yes, but for example, in my practical use, I analyze one alkane sample before the sequence for biological samples is started.
Then, I make the alkane dictionary file. Then, the file is used to calculate RI values for all of biological samples data.

>> do I really need alkanes in each sample?
No, but in my practical use, the alkane sample is analyzed "each batch sequence". Maybe, for a large-scale project, in my experience, 50-60 samples were analyzed each week (in which one alkane mixture is also analyzed), then, a total of 1000 biological samples was analyzed by MS-DIAL. Then, I prepared the alkane dictionary file to calculate RI values for "the week's biological samples peaks". Then, the RI values were used for annotation and for peak alignment.

Just for your information.
Hiroshi

Re: The use of RI for Alignment and Identification

Reply #3
Dear Hiroshi,

thanks for your giving insights into your routine! This is the way I do it as well. So there must be something in my alkane dictionary.

Now that you reported on the fact that MS Dial does not need the alkane in each sample I will investigate my problem more deeply.

Thank you for your assistance and the work I you are investing into the tool,

Stefan