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Messages - Angrist

2
MS-DIAL / Re: Gangliosides and Incorrect Charge Status
Dear Hiroshi
thanks for the quick reply.
It would actually be GD2. Given the importance in the clinic of this marker, as in the diagnosis of Neuroblastoma, would it be possible to include this class of lipids as well? HMDB reports almost 30 of them and only one is verified to be present in plasma, which in my opinion should be further investigated, as well as some acetylated or modified lipids. I think GD1 and GD3 might also be of considerable interest.
Is there any possibility of these integrations?
all the best
Andrea


3
MS-DIAL / Gangliosides and Incorrect Charge Status
Dear Developers
I am working on a lipidomics study of cancer patients plasma. Before starting with the untargeted acquisition, I did some tests on lipid standards and I found that on a particularly large ganglioside (over 1600 Da) MSDIAL can not recognize the bicaric state of the molecule, even if it is markedly evident, and then it tries a misidentification as if it were M- and not M2-. I don't understand the reason. I can safely share the raw files as the MSDIAL session.
all the best
Andrea
4
MS-DIAL / Infusion and MSDIAL
Dear Developers
I will soon have the opportunity to analyze several hundred infused biological samples. I was wondering if MSDIAL is capable of handling data of this type, effectively lacking chromatography.
all the best
Andrea
5
MS-DIAL / Batch job error
dear Developers
During the MS Finder search on all MS/MS events (including the identified ones) I received the following error:

Batch job was desorbed by the following error: Object reference not set to an instance of an object

what does it mean? what are the measures to avoid it again? the processing time is very long, even if I indicated in the configuration a time out of 1 min (structure finder stopped at 255075933 after 2 day..)
all the best
andrea
6
MS-DIAL / new features on File Property Setting
Dear Developers
some suggestions in reference to the "File Property Setting":
1) have the possibility to select\deselect all files with only one flag.
2) select \ deselect files using only the group they belong to (QC, Control, Treated etc..).
these simple features would simplify a lot the work on wide samples avoiding stupid selection errors.

I would like if it was possible to have a clarification on column Y varaibile 0-1.

all the best
Andrea
7
MS-DIAL / Tables
Dear Developers
In the "Show ion table" the functions "Annotated Compound Table" and "Spot Relation Table" are not clear to me. My difficulty is to understand exactly what they refer to and how to use them.
thanks for your time
Andrea
8
MS-DIAL / Re: MSP
thank you very much
9
MS-DIAL / MSP
thanks to the developers to make our work easier and more efficient.
I have three questions about spectral library management.
1) on the site (http://prime.psc.riken.jp/compms/msdial/main.html#MSP) there are the new databases, Last edited in Aug.14th, 2020. If I try to open, for example, "All public MS/MS (12,879 unique compounds) MS/MS Negative 36,848 records" in MS-Lima I get a long line of errors. why?
2) Wouldn't it be very useful and simpler if MSDIAL could integrate the search on different MSP files at the same time, without having to do any merging of the different db? Keeping the public MSP file fixed, downloadable from prime.psc.riken.jp, I could integrate it with small, new, and customized libraries!
3) in case I want to merge two MSPs what is the procedure?
thanks for your work
Andrea
10
MS-DIAL / Re: internal Standard
this time it was my turn to be sick!
thank you very much for your kind and complete reply.
I also take this opportunity to ask for clarification on "correlation-based deconvolution" and the 4 possibilities "Setting and run", "Identification",  "Run single spot" and "Show CorrDec Spectra". I would like to understand when they should be used and with what attention.
thanks again for your wonderful work.
11
MS-DIAL / internal Standard
Dear developers,
I would like to better understand how and where to set the information of the internal calibrants to make the normalization of chromatographic runs.
I would also like to understand what they are and how to use the parameters that show ion table and specifically Fill and Correlation
Thanks for your work, you have created a software which is the MaxQuant of Metabolomics! 8)
all the best