MSnLib Mass spectral libraries (.mgf and .json)

<p>The data for <a href="https://doi.org/10.26434/chemrxiv-2024-l1tqh-v2">MSnLib</a> are divided into several Zenodo records due to size constraints.&nbsp;</p> <p>raw positive: <a href="https://doi.org/10.5281/zenodo.10966404">10966404</a><br>raw negative: <a href="https://doi.org/10.5281/zenodo.10967081">10967081</a><br>mzml positive and negative: <a href="https://doi.org/10.5281/zenodo.10966280">10966280</a><br>spectral libraries: <a href="https://doi.org/10.5281/zenodo.11163380">11163380</a></p> <p>This record includes the automatically generated spectral libraries (MSnLib) within mzmine, acquired using a flow injection method on an Orbitrap ID-X instrument, for all compound libraries. There are multiple files for each compound library containing MS2 only or MSn in two data formats (.mgf or .json) for both polarities.&nbsp;</p> <p>MS2 contains next to all MS2 spectra all pseudo MS2 spectra (a full MSn tree merged into one spectrum per compound ion). MSn contains all individual MSn stages additionally. The first number for each file highlights the library building date.</p> <p>9 Compound Libraries:</p> <ul> <li>Short Name: Full name, Provider (Catalog number), total compounds (not all detected during library building)</li> <li>MCEBIO: Bioactive Compound Library, MedChemExpress (HY-L001), 10,315 compounds</li> <li>MCESAF: 5k Scaffold Library, MedChemExpress, (HY-L902), 4998 compounds</li> <li>NIHNP: NIH NPAC ACONN collection of NP, NIH/NCATS, 3988 compounds</li> <li>OTAVAPEP: Alpha-helix Peptiomimetic Library, OTAVAchemicals (a-helix-Peptido), 1298 compounds</li> <li>ENAMDISC: Discovery Diversity Set -10, Enamine (DDS-10), 10,240 compounds</li> <li>ENAMMOL: Carboxylic Acid Fragment Library + Random, Enamine and Molport, 4378 compounds</li> <li>MCEDRUG: FDA-Approved Drug Library, MedChemExpress (HY-L022), 2610 compounds</li> <li>MCEDIV_50k_Sub: Subset of 50K Diversity Library, MedChemExpress (HY-L901), 20000 compounds</li> <li>TargetMolHTSNP: Subset of Natural Product Library for HTS, TargetMol (L6000), 2175 compounds</li> </ul> <p>Information regarding the SPECTYPE</p> <ul> <li>no SPECTYPE or SINGLE_BEST_SCAN: Best spectrum for each precursor and energy (highest TIC)</li> <li>'SAME_ENERGY' = Additionally, if a spectrum was acquired multiple times for a precursor with the same energy, they are merged into one spectrum only with the same energy (max. signal height used for each fragment signal).</li> <li>'ALL_ENERGIES' = merged spectrum of all used energies (in our case 3 for each precursor, using the merged (same energy) if available).</li> <li>'ALL_MSN_TO_PSEUDO_MS2' = mzmine merges all MSn into one pseudo MS2.</li> </ul> <p>&nbsp;</p> <p>MCEDIV and TargetmolNPHTS&nbsp;</p>