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Topics - Bernadette

1
MS-DIAL / GC retention index
Hello everyone,

I am working with GC and use Alkane standards to get retention indices.  In the MS-DIAL tutorial it is explained, how the retention indices are calculated. However, I can't find info on how extrapolation is done. For example, my Alkane index file is starting from C8 but MS-DIAL is then also calculating retention indices for compounds with lower retention time.
I hope someone can explain to me how this is calculated.

Thank you!
Bernadette
2
MS-DIAL / S/N ratio
Dear all,

I am working with GC-TOFMS data and have some questions regarding the S/N ratio.
I have exported two files from the Alignment result:
(1)   exported Raw data matrix (Area)
(2)   S/N matrix
In (1) I have the column S/N average for each Alignment ID. But when I look at the S/N ratios in (2) and calculate the average for each Alignment ID there, I get different values.
When I look then at the Peak list for a specific sample, I see different S/N ratios compared to the (2) S/N matrix.
So, I am wondering, how the S/N ratio is calculated in MSDial? It is also hard to evaluate the noise, because when you look in the alignment spot viewer at the chromatogram, you only see the zoomed peak and not the baseline. 

It would be very helpful, if someone can explain this.

Best regards,
Bernadette
3
MS-DIAL / Peak count filter - GC-MS project
Hello everyone,

I am working on GC-TOFMS data with different sample groups and I am trying to understand, what the peak count filter means. According to the tutorial, it should remove peaks that are not fully detected in the alignment. But I don’t really understand, how this parameter deals with different sample groups – does it work group-wise or does it take simply all samples (regardless of the group they belong to) into account?
For LC data, there is the additional option N% detected in at least one group but this is not available in a GC project.
I hope you can help me.

Best regards
Bernadette