when I saw the title of this section I was sure that my request fits in here. After reading some of the other post I became sceptical but still I would like to place my question somewhere.
I found some interesting Peaks in my GC-EI-TOF data (MEOX + TMS derivatized polar extracts of natural microbial communities) and the library's couldn't help in understanding the compound I found here. The RI of the requested analyte is 2003.3 and I have a very similar spectrum occuring at RI 2055.2. It seems to me that there one analyte with different configurations (like the sugars) but m/z 278 is a black box for me. Does anyone knows which fragment m/z 278 typically represents? Or can someone help me with the compound class?
You can find the spectrum table of this compound attached to this post. Many thanks for any comment!
my questions might be annoying to the expert users but I still have a longer wish list for MS-DIAL
These days I have realized that MS-DIAL does not remove samples from the statistics that lack the normalization STD. In my case I analyzed some solvent blanks which I treated as additional blanks (beside my process blanks). When I normalize to my internal STD almost all peaks are normalized, except for these blanks. This is a plausible behaviour but a further analysis of these (non-normalized) samples should be avoided, right?
What if MS-Dial deselects all samples that haven't been normalized properly for the further analysis?
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).
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?
I have discovered something weird in the MS Dial tool and I am highly interested in your experiences with following issue:
I used the retention time for alignment and the retention time tolerance was set to 0.075 min (4.5 seconds). Then the exported retention time matrix of the aligned peaks was checked for differences in retention time (min, max, range) and I have discovered that there were Peaks aligned which were several minutes apart. Please have a look to the screenshot of the export RT table: high_diff_in_RT.PNG. In the frist line I marked a peak which has a RT of 7.9 min and this was aligned with 5.9 min RT peaks... This is even worse than the statistical compare tool of LECO and I am very sceptical that this is the usual output. Has anyone experienced the same? Why should set up a tolerance value if this is ignored by the aligning algorithm?!
Please have a look to your data and tell me if you have experienced similar results!
great to a format like this for asking questions. I just started playing around with MS DIAL and the tool looks very promising to me (at least the software includes all the steps I did with my data on a different platform).
But when I process the demo dataset "Alkanes Kovats deom by Arabidopsis" I fail to achieve the same results as it is shown in the tutorial. I am using Version 4.24 on a Win10 and I followed the tutorial carefully but Alignment Spot Viewer stays empty and also the Rep. vs Ref. Window does not show any Refence (but instead "No information"). It seems that the "GCMS DB_MassBank-Restek-RIKEN.msp" was not considered for comparison. May someone else try to run the Demo dataset? If I use RT instead of RI for the alignment I obtain results for the alignment but the Identification remains open. So the problem might be related to the usage of RI.
I also tried to align data that I have obtained myself and the Alignment Spot viewer gave reasonable results. Therefore the software itself seems to work fine...