Deep Learning-Enabled MS/MS Spectrum Prediction Facilitates Automated Identification Of Novel Psychoactive Substances

Fei Wang, Daniel Pasin, Michael A. Skinnider, Jaanus Liigand, Jan Niklas Kleis, David Brown, Eponine Oler, Tanvir Sajed, Vasuk Gautam, Stephen Harrison, Russell Greiner, Leonard J. Foster, Petur Weihe Dalsgaard, David S. Wishart

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


The market for illicit drugs has been reshaped by the emergence of more than 1100 new psychoactive substances (NPS) over the past decade, posing a major challenge to the forensic and toxicological laboratories tasked with detecting and identifying them. Tandem mass spectrometry (MS/MS) is the primary method used to screen for NPS within seized materials or biological samples. The most contemporary workflows necessitate labor-intensive and expensive MS/MS reference standards, which may not be available for recently emerged NPS on the illicit market. Here, we present NPS-MS, a deep learning method capable of accurately predicting the MS/MS spectra of known and hypothesized NPS from their chemical structures alone. NPS-MS is trained by transfer learning from a generic MS/MS prediction model on a large data set of MS/MS spectra. We show that this approach enables a more accurate identification of NPS from experimentally acquired MS/MS spectra than any existing method. We demonstrate the application of NPS-MS to identify a novel derivative of phencyclidine (PCP) within an unknown powder seized in Denmark without the use of any reference standards. We anticipate that NPS-MS will allow forensic laboratories to identify more rapidly both known and newly emerging NPS. NPS-MS is available as a web server at, which provides MS/MS spectra prediction capabilities for given NPS compounds. Additionally, it offers MS/MS spectra identification against a vast database comprising approximately 8.7 million predicted NPS compounds from DarkNPS and 24.5 million predicted ESI-QToF-MS/MS spectra for these compounds.

Original languageEnglish (US)
Pages (from-to)18326-18334
Number of pages9
JournalAnalytical Chemistry
Issue number50
StatePublished - Dec 19 2023

All Science Journal Classification (ASJC) codes

  • Analytical Chemistry


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