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@jmr-nist-gov jmr-nist-gov released this 20 Jul 16:09
· 25 commits to main since this release
v1.0.1-202307
75bb6ba

Initial Release

This is the first official release of the Database Infrastructure for Mass Spectrometry (DIMSpec) project supporting non-targeted analysis. At this time DIMSpec is distributed as a project for extensibility and customization supporting individual stakeholder use cases.

Tools

As of this release, DIMSpec supports the following:

  1. Simplified project set up via installation script (see R/compliance.R) tested on both Windows and Ubuntu operating systems.
  2. Rapid build, iteration, and rebuild of portable databases for multiple projects and endpoints.
  3. An application programming interface able to be hosted on a network.
  4. Automatic logging and function argument verification (these may be easily disabled to improve performance).
  5. Three web applications able to be hosted on a network:
    • Table Explorer for schema entity exploration;
    • Mass Spectral Quality Control (MSQC) for evaluation of quality metrics for annotated data; and
    • Mass Spectral Match (MSMatch) for comparing user experimental data against a DIMSpec library including fragment matching.
  6. Integration of chemometrics support through RDKit and a suite of custom non-targeted analysis tools written in R.
  7. Fully extensible codebase using only open-source products, with all available objects transparently provided to a working session.
  8. Complete support for offline use including local help files and documentation.

Documentation

A comprehensive user guide is available including function documentation. All documentation is made available from the project once loaded, with convenience functions to view the user guide, function reference document, and within-IDE function documentation.

Data

The current demonstration database includes mass spectra for per- and polyfluoroalkyl substances (PFAS). These are held in an SQLite relational database and includes curated MS1 and MS2 mass spectral data for 132 distinct PFAS analytes represented by 351 peaks across 104 samples from various sources. Instrument method, quality assurance metrics, and sample metadata are included for interpretation context. The same database will soon be available for download directly from the NIST Public Data Repository.

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