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Stortebecker / metabolomics

A repo to exchange and discuss metabolomics issues at the ZBSA Freiburg.
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Converting NIST db files to .msp #4

Open Stortebecker opened 7 years ago

Stortebecker commented 7 years ago

The commercial NIST db is provided in a closed Nist db file format. The freeware NIST MS search allows to export spectra to the open .msp format. However, conversion is restricted to 1,000 spectra. The whole database consists of approx. 200,000 spectra.

It would be helpful to convert the full db to be able to modify it and use it with open software. @korseby @blankclemens Can we come up with a cunning way to do so? A simple batch script might be sufficient, if the NIST MS search can be controlled via API.

Stortebecker commented 7 years ago

Of course, we cannot provide the converted database publicly. But it could be provided for people owning a NIST db licence.

Stortebecker commented 7 years ago

I guess that this issue could be solved by using either the MSeasy R Package, the NIST MS PepSearch or the PyNISTPL. See links in #9 .

Stortebecker commented 7 years ago

Another way would be to use the NIST MS Search API directly: Instructions (PDF)

gtmddly commented 6 years ago

Hello, I am a college student.，I am doing research on this subject for graduation，and I am interested in your research. Could you please send me a document of MSP format?Here is my email ：1357611445@qq.com Thank you for your generosity.

hechth commented 3 years ago

Has anyone done some work on this?