DreaMS Search

DreaMS (Deep Representations Empowering the Annotation of Mass Spectra) is a transformer-based neural network designed to interpret tandem mass spectrometry (MS/MS) data (Bushuiev et al., Nature Biotechnology, 2025). This website provides an easy access to perform spectral library searches to identify small molecules or their analogue candidates by querying MassSpecGym spectral library (combination of GNPS, MoNA, and Pluskal lab data) or custom MS/MS datasets.

Upload MS/MS file

Drop your MS/MS file here

or click to browse

.mgf.mzML.mzXML.hdf5

Choose datasets

Pick one or more reference libraries to search against.

Advanced settings

Advanced settings (optional)

Top-K hitsMatches returned per spectrum.

Similarity thresholdMinimum DreaMS similarity to report.

Calculate modified cosine similarity

Enable to also calculate traditional modified cosine similarity scores between the input spectra and library hits (a bit slower)

Only predict on high-quality input spectra

Enable to exclude low-quality input spectra before prediction. MS/MS spectrum is considered low-quality if it does not satisfy quality criteria "A" as defined in the DreaMS paper (Fig. 2b).

Upload MS/MS file

Choose datasets

Advanced settings

Run DreaMS Search