v1.8.0

This release brings support for more search and quantification engine outputs (alphaDIA v2.0.0, directLFQ, MSFragger) as well as extended SMILES support for various protein modifications + tags .

What's Changed

New Features

• NEW: annotating real spectra vs calculated one by @boopthesnoot in #314
• directLFQ protein group reader by @lucas-diedrich in #365
• Alphadia precursor ID support by @lucas-diedrich in #368
• alphaDIA v2.0.0 PSM table support by @lucas-diedrich in #369
• Add msfragger tsv reader by @GeorgWa in #367
• Add NHS modifications by @GeorgWa in #375
• Enable msfragger modification mapping by @GeorgWa in #376
• Add mtraq modifications by @GeorgWa in #377
• Add TMT 10plex modifications by @GeorgWa in #378
• Add itraq modifications by @GeorgWa in #379
• Use placeholder Atom for N-term modifications by @GeorgWa in #381
• add dileu modifications by @GeorgWa in #380
• Add modification_mapping support to MSFragger reader by @GeorgWa in #371
• feat: add Ammonia-loss@C^Any_N-term support for MSFragger by @GeorgWa in #390
• feat: add ion mobility column mapping to MSFragger PSM TSV reader by @GeorgWa in #383
• add dimethyl isotope label by @GeorgWa in #382
• feat: add lactyl and formyl modifications with SMILES by @GeorgWa in #384
• feat: add N-ethylmaleimide (NEM) SMILES and msfragger mapping by @GeorgWa in #385
• feat: add PSMtag light modification for K and N-term by @GeorgWa in #388
• Register all modifications for msfragger reader by @GeorgWa in #389

Fixes

• Fix get cut positions by @mschwoer in #366

Documentation

• Adapt scverse tutorial to alphadia v2.0.0 by @lucas-diedrich in #370

Maintenance

• [VERSION] Bump version to 1.7.5-dev0 (merge after release) by @github-actions[bot] in #364
• [VERSION] Bump version to 1.8.0 by @github-actions[bot] in #394

Other Changes / unlabeled

• Remove call pattern by @GeorgWa in #372
• Shameless Claude test coverage for ModificationMapper by @GeorgWa in #373
• Shameless Claude modification constants added by @GeorgWa in #374
• Correct digly handling with SMILES by @GeorgWa in #386
• refactor: use [Lv] placeholder for N-term mod SMILES by @GeorgWa in #387
• Document MSFragger mass truncation convention by @GeorgWa in #391
• AX797: Rename local variables to distinguish boolean from string types by @lucas-diedrich in #393

Full Changelog: v1.7.4...v1.8.0