Enveda-180: generation of a large open multimodal MS/MS and ion mobility spectral library for drug-like small molecules

Description

Technical info (English)

Enveda-180 is a curated tandem-MS spectral library generated from high-throughput, pooled LC-MS/MS profiling of the Enamine HLL-200 hit-locator collection. The release comprises 1,158,293 curated MS/MS spectra for 184,330 unique compounds (distinct full InChIKeys; 183,476 distinct InChIKey-14 connectivity blocks). Each compound is represented by a median of 6 spectra (mean 6.28, maximum 48), and 99.3% of compounds carry two or more spectra.

Acquisition. Data were acquired on a Bruker timsTOF Pro 2 trapped-ion-mobility Q-TOF operating in PASEF mode, under heated electrospray ionization (300 °C, 4500 V) in both positive and negative ion modes. Full-scan range was m/z 20 to 1300 with an ion-mobility range of 0.3 to 1.45 V·s·cm⁻². Each selected precursor was fragmented at three nominal collision energies (20, 40, 60 eV). Liquid chromatography used a Waters ACQUITY Premier BEH C18 column (2.1 × 50 mm, 1.7 µm) with water and acetonitrile mobile phases containing 0.1% formic acid, a 5% to 95% acetonitrile gradient over 5.5 minutes (7 minutes total), 0.5 mL/min flow, and a 5 µL injection.

Adducts and polarity. Spectra span 14 adducts across both polarities (ESI+ 77.0%, ESI− 23.0%). [M+H]+ and [M−H]− together account for roughly 67% of all spectra. The full distribution:

Ion mobility and CCS. 96% of spectra carry an experimental collision cross section derived from calibrated 1/K0 reference points. Enveda-180 reports multiple mobility-resolved CCS values per precursor rather than a single value: among CCS-bearing spectra, 56% carry two or more species and 31.5% carry three or more, with a median inter-species ΔCCS of 11.8 Ų (6.6% of the primary CCS). These secondary species capture protomers, isomers, conformers, and monomer/dimer pairs that share a nominal m/z and retention time.

Spectral quality. Spectra passed multi-criteria curation combining SIRIUS rank-1 fragmentation-tree scoring, explained-intensity and minimum-peak thresholds, precursor-integrity checks, and round-trip InChIKey validation. The rank-1 tree explains a median of 88.6% of total fragment intensity; 91.4% of spectra exceed the 70% explained-intensity level targeted by manual annotators, and 98.1% exceed 50%. Median normalized spectral entropy is 0.44. Spectra contain a median of 138 peaks (minimum 4). We also provide an intensity-filtered version of the spectra, with fragment peaks below 1% relative intensity removed.

Files and identifiers. The release ships MGF, MSP, JSONL and Parquet serializations of the spectra. Each spectrum has a unique, sortable identifier of the form enveda_<compound index>_<spectrum index>.