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Public Workflows at GNPS
https://gnps.ucsd.edu/
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[GC] Public GC libraries release at GNPS #89

Closed mwang87 closed 4 years ago

mwang87 commented 5 years ago

@aaksenov1 Please list all the libraries that we intend to make public here.

mwang87 commented 4 years ago

I need

aaksenov1 commented 4 years ago

1. Library Name: Fiehn Library Description: Mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry. Compiled 2,212 electron impact mass spectra and retention indices for quadrupole and time-of-flight GC/MS for over 1,000 primary metabolites below 550 Da, covering lipids, amino acids, fatty acids, amines, alcohols, sugars, amino-sugars, sugar alcohols, sugar acids, organic phosphates, hydroxyl acids, aromatics, purines and sterols as methoximated and trimethylsilylated mass spectra under electron impact ionization. Link to Library: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=a99963ddcb314887afaa61e2bf894823

  1. Library Name: HMDB Library Description: The Human Metabolome Database or HMDB (www.hmdb.ca) is a web-enabled metabolomic database containing comprehensive information about human metabolites along with their biological roles, physiological concentrations, disease associations, chemical reactions, metabolic pathways, and reference spectra. Link to Library: http://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=27eb6967918041199110239b436f8be3

  2. Library Name: MoNA Library Description: GC-MS portion of the MassBank of North America (MoNA) database. MoNA is a metadata-centric, auto-curating repository designed for efficient storage and querying of mass spectral records. It intends to serve as a the framework for a centralized, collaborative database of metabolite mass spectra, metadata and associated compounds. MoNA currently contains over 14K mass spectral records from experimental libraries as well as from user contributions. Link to Library: http://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=58c04d109dae48a9a2ff1cf08e4a0b6f

mwang87 commented 4 years ago

We will put these libraries at CCMS_SpectralLibraries/GNPS_GC_Libraries

We will call the above libraries

  1. GC-FIEHN
  2. GC-HMDB
  3. GC-MONA
mwang87 commented 4 years ago

Outstanding tasks

mwang87 commented 4 years ago

Do we have references for each of the entries so we can link to the original resource? @aaksenov1

mwang87 commented 4 years ago

Deployed and ready to use.

aaksenov1 commented 4 years ago

Search works, matches look good. Example job: https://proteomics2.ucsd.edu/ProteoSAFe/status.jsp?task=d255788d2b8f472881cfc95cd8017c8a