v0.11.0

What's Changed

This is the biggest release yet - major overhaul to LFQ, changes to chimeric searching!
Please note that there are some breaking changes to the quant section of the configuration file format

It is possible that the changelog below (and in CHANGELOG.md) are not completely comprehensive, please open an issue if you discover something.

LFQ actually works pretty well now: 🎯 🚀

Added

• Support for percolator output files (--write-pin CLI flag)
• Support for modifying file batch size (--batch-size N CLI flag)
• Add delta_best feature, which reports the delta hyperscore from the best match to current ranked PSM
• Add Sage version to results.json files

Changed

• Rename "file" to "filename" in quant.tsv by @lgatto in #57
• Breaking changes to quant section of the configuration file format
• Rename delta_hyperscore to delta_next
• Altered internal scoring algorithm. Rather than consider all MS2 peaks within a m/z tolerance window to be matches to a theoretical spectrum, consider only the closest peak. This should increase the accuracy of # of matched peaks, and subsequent scores
• Overhaul of chimeric scoring, report_psms can now be used to search for multiple chimeric spectra
• Completely overhauled the LFQ algorithm: added match-between runs, peak scoring using normalized spectral angle relative to theoretical isotopic envelope, target decoy scoring of MS1 integration
• Fixed bug in picked-peptide FDR that could lead to liberal FDR
• Fixed bug in picked-protein FDR that could lead to conservative FDR
• Fixed bug where using variable protein terminal (e.g. protein N-terminal acetylation) modifications could cause some determinism. This also improves the accuracy of peptide => protein assignment. Unfortunately this fix has performance implications, causing creation of the fragment index to take up to ~2x as long.

Removed

• Remove no-parallel CLI flag, and parallel configuration file entry

Full Changelog: v0.10.0...v0.11.0