Table 2. List of important databases and tools.
| Databases and software | Use case | Data available/input data | Key features |
|---|---|---|---|
| Database | |||
| NCBI | Biological sequences | DNA, RNA, amino acid | Repository of various biological sequences |
| Dictionary of Natural Products a | Physicochemical data | Solubility, UV–Vis | Extensive database resource of natural products and their physiochemical properties |
| Software for in silico annotation | |||
| antiSMASH | RiPPs and NRPs | DNA | Rule-based cluster detection |
| SANDPUMA | NRPs | DNA | A-domain specificity prediction |
| DeepBGC | RiPPs and NRPs | DNA | Gene cluster detection |
| Software for peptidogenetic pipelines | |||
| DeepRiPP | RiPPs | DNA (open reading frame) | Classification, processing and spectral matching |
| Software for mass spectrometry analysis | |||
| DEREPLICATOR+ | RiPPs and NRPs | LC-MS/MS | data Natural product identification from mass spectrometry spectra (GNPS framework) |
| MS-FINDER | Mass spectrometry data analysis | EI-MS, GC-MS, MS/MS | Formula predictions, fragment annotations and structure elucidation |
| Software for MSIa | |||
| MSiReader | Mass spectrometry data analysis | MSI | MSI platform for analysis |
| SCiLS Lab a | Mass spectrometry data analysis | MSI | MSI platform |
| ImageQuest a | Mass spectrometry data analysis | MSI | MSI platform |
| High Definition Imaging a | Mass spectrometry data analysis | MSI | MSI platform |
| msiQuant | Mass spectrometry data analysis | MSI | MSI platform for analysis |
Various resources can aid in peptidomics and one of the main resources most researchers start with are biological sequence databases, to gather genomic (DNA), transcriptomic (RNA), proteomic (amino acid) or other data that may be relevant to their research. These data types can be further complemented by specialized software or other physiochemical or spectral data to make more accurate predictions or annotations of peptides that may be present in the sample. Databases and further tools are continued in Supplementary Table 1. A-domain, adenylation domain; EI-MS, electron ionization–mass spectrometry; GC-MS, gas chromatography–mass spectrometry; LC-MS, liquid chromatography–mass spectrometry; MSI, mass spectrometry imaging; MS-MS, tandem mass spectrometry; NRP, non-ribosomally synthesized peptide; RiPP, ribosomally synthesized and post-translationally modified peptide.
Commercial platforms, may be subject to licensing charges.