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1
MS-DIAL / Re: MS-Dial lipid RTs: Is there a published LC method RTs are derived from?
Last post by AnaCarolina-RosadaSilva -
Hey Brian.

They have described all the methods that they tested on their paper: https://www.nature.com/articles/s41587-020-0531-2

Also, in the identification tab you can choose to not consider RT, for example:
Retention time tolerance   100 min

I am used to doing that. There are all the parameters to LC-MS data on my published paper (https://doi.org/10.1016/j.foodres.2020.109727).


Best Regards,
Ana Carolina
3
MS-DIAL / Re: MS-DIAL 4.70 and MS-FINDER 3.52 were released.
Last post by spapaz -
Dear Hiroshi

thank you for this update.

I was wondering if, with this new version, direct import works for both SCIEX .WIFF and .WIFF2 formats,
or if the WIFF2 still needs conversion to ABF (and in this case, do we need to first convert it to centroid mzML)?

And, is this information from the FAQ still up do date:
"Unfortunately, the current work flow does not work for SWATH-MS data yet although it can be processed in MS_DIAL to get MS1 information in MS-DIAL. After SCIEX releases the Software Developer Kit which is needed for modification of ABF converter, the flow will become easier and SWATH-MS data can be also imported".
http://prime.psc.riken.jp/compms/msdial/faq.html

Also, thank you for the FAQ page which is very useful. Given how fast you introduce new versions, could you perhaps indicate the date on the page? 

Thank you again

Stefano


4
MS-DIAL / mass shift
Last post by kljw001 -
Hi all,

We are using Agilent 6560 IM-QTOF to run some standard compounds to generate in-house library.

After using MS-Dial to extract peak information, a lot of compounds have a big mass shift which is around 20 ppm (the mass accuracy in raw file (.d) is less than 5 ppm).
We have tried different importing methods, including directly drag and drop it into the MSDial or convert it to ibf file first, but both methods give us the same problem (mass shift). I am wondering if anyone also has the same problem and how you address it.

Thanks in advance.
 
5
MS-DIAL / MRMPROBS-error
Last post by Artur -
I am a user of MRMPROBS.
I try to analyze the data, but I get an error and cannot proceed.
Unfortunately, the error window is too long to see the details.
Can anyone tell me what I need to improve?
6
MS-DIAL / MS-DIAL could not export alignment to GNPS format
Last post by Bambang -
Dear MS-DIAL developer,
I have a problem when exporting the alignment result to GNPS, as shown in the screenshot. The GNPS export menu did not applicable. In this case, I use GC-MS untargeted analysis, centroid format.
Would you mind explaining this issue?

Regards,
Bambang Wijayanto
7
MS-DIAL / means of circle with different size and color for molecular spectrum networking
Last post by Bruce -
Dear everyone,
Can everyone have the experience of using the function of molecular spectrum networking of MS-dial, what is the algorithm to judge or search the compound.
Besides, what is the meaning of the circle with different color, size(related to the abundance?) and distance (similarity?).

I try to use it to search the compound with similar structure for one target compound, but sometimes, the compounds proposed by the software had any similar fragmental ions compare to the target fragmental ions, why? Can anyone kindly give some suggestions for me!
thanks!
Bruce
8
Task groups / Cell pellet extraction
Last post by aperalbom -
Hi all!
Is there anyone working with pellet (from cell lines)? Which protocols can be used for metabolomics extraction?