search

MassBank / MassBank-data

Official repository of open data MassBank records
69 stars 56 forks source link

.mlb export #27

Open joerg-b opened 5 years ago

joerg-b commented 5 years ago

Dear MassBank team, I would very much like to use the MassBank data in .mlb format so that I can use Bruker's Library Editor to review and manipulate the library. In the next step I then would like to use sub-libraries of compounds that are more likely to be contained in my samples when I process my data using Bruker's DataAnalysis and Metaboscape. Thanks for considering my request. Best regards, Joerg

Treutler commented 5 years ago

Dear Joerg, what sub-set of compounds would you be interested in? Species specific compounds, certain compound classes, certain chromatographies? Best, Hendrik

joerg-b commented 5 years ago

Dear Hendrik, I'm looking more for the origin of the compounds and I'm generally only interested in compounds that can occur in mammalian cells or body fluids. For example, I would remove any compound that contains F/Cl/Br/Sulfate because they don't occur in mammalian primary metabolism. Moreover I would try to remove secondary plant metabolites, but I don't have a good rule for that. Maybe anything with more than 20 O, any non-lipid larger than 1200 Da... Best Joerg

tsufz commented 5 years ago

Hi Joerg and all, I guess, this needs some re-tagging of all compounds. With our environmental spectra from UFZ and Eawag it is quite easy as we tagged all as environmental standard. The other compounds need to be curated in order to in the different categeries if no species is given. We have the species tag, but it is scarcely used if I remember correctly.

Best, Tobias

joerg-b commented 5 years ago

Hi Tobias,

I was more thinking along the lines of filtering on sub-strings of the sum formula or the monoisotopic mass. That wouldn't be perfect but should get quite a few of the cases that I mentioned.

Best Joerg

On 27.09.18 19:22, Tobias Schulze wrote:

Hi Joerg and all, I guess, this needs some re-tagging of all compounds. With our environmental spectra from UFZ and Eawag it is quite easy as we tagged all as environmental standard. The other compounds need to be curated in order to in the different categeries if no species is given. We have the species tag, but it is scarcely used if I remember correctly.

Best, Tobias

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/MassBank/MassBank-data/issues/27#issuecomment-425174596, or mute the thread https://github.com/notifications/unsubscribe-auth/AlcVHOvHLN9HUb6QWdFJypxPjdKPjm69ks5ufQlhgaJpZM4W6r92.