Sage Plus v0.1.0-beta.16

First public launch release. Benchmarks against upstream Sage v0.15.0-beta.2 are in benchmarks/HEADTOHEAD.md. On four PXD028735 HYE files, Sage Plus found +1.2% PSMs and peptides and +1.6% protein groups at 1% FDR, used 6.2 GiB vs 7.5 GiB peak memory, and gave equal LFQ ratios.

Upgrading: search-space settings are now required (see Changed). Run sage --write-config list for starting configs.

Changed

• Breaking: search-space settings must be stated. database.static_mods (may be {}),
  database.ion_kinds, and, when a FASTA is digested, database.enzyme with cleave_at,
  restrict, missed_cleavages and semi_enzymatic no longer have defaults. A missing setting
  is an error naming it, with a snippet to paste. The old implicit values were: no enzyme block =
  trypsin, 0 missed cleavages, restrict: "P"; partial block = 1 missed cleavage, restrict: "";
  no static mods; b and y ions. The JSON Schema marks the same fields required.
• Committed configurations, tests and benchmark generators state these settings explicitly.

Added

• sage --write-config <NAME> [PATH] writes a starting configuration: minimal, full,
  trypsin-hcd, trypsin-hcd-tmt, phospho, etd or nonspecific (list shows them).
  Without PATH it prints to standard output; an existing file is replaced only with
  --overwrite. Every preset is tested to pass validation.
• "missed_cleavages": "unlimited" keeps every peptide within the length and mass limits.
• "max_len": "unlimited" bounds peptide length only by peptide_max_mass and the 255-residue
  encoding limit. Sage logs one warning when it is combined with unlimited missed cleavages or a
  non-specific digest (cleave_at: "").
• Startup logs, at info level, the defaults used for search-space settings left unset.

Fixed

• The fragment index no longer panics past 4,294,967,295 fragments. Bucket offsets are 64-bit
  (24-byte buckets, one per up to bucket_size fragments), so the only index cap left is the
  32-bit peptide index inherited from Sage.

• A missing input file or FASTA names the path: cannot open `/x/y.mzML`: No such file or directory. An output directory that cannot be created is named the same way.

• A search whose database has no target peptides fails instead of exiting 0 with empty results.
  The error names the length and mass ranges in force. enzyme.min_len above max_len, or
  peptide_min_mass above peptide_max_mass, is rejected when the configuration is validated.

• missed_cleavages above 254 no longer overflows. In a release build 255 wrapped and searched
  as 0 missed cleavages.

Removed

• Telemetry. Sage Plus no longer sends run statistics to upstream Sage's endpoint, and the
  reqwest dependency is gone. --disable-telemetry-i-dont-want-to-improve-sage is still
  accepted as a hidden no-op so existing scripts keep working. Runner::run and
  run_with_summary return the RunSummary, and JobResult has no telemetry field.
• min_free_memory_gb from seven benchmark configurations; Sage already ignored it.

Documentation

• benchmarks/HEADTOHEAD.md: Beta 16 against upstream Sage v0.15.0-beta.2 on four PXD028735 HYE
  runs with one shared config. Sage Plus finds 1.2% more PSMs and peptides and 1.6% more protein
  groups at 1%, peaks at 6.2 vs 7.5 GiB, and matches upstream's LFQ species-ratio accuracy.
• Initiator Met clipping re-measured on HEK SILAC: +3.4% PSMs at 1% when protein N-terminal
  acetylation is searched, +0.2% when it is not. README and DOCS state the condition.
• README rewritten for new users: measured results, install options and a quickstart.
  Internal design notes moved to docs/design/ and old benchmark notes to benchmarks/archive/.

Full Changelog: v0.1.0-beta.15...v0.1.0-beta.16

Sage Plus v0.1.0-beta.15

Full Changelog: v0.1.0-beta.14...v0.1.0-beta.15

Sage Plus v0.1.0-beta.14

Full Changelog: v0.1.0-beta.13...v0.1.0-beta.14

Sage Plus v0.1.0-beta.13

Full Changelog: v0.1.0-beta.12...v0.1.0-beta.13

Sage Plus v0.1.0-beta.12

Full Changelog: v0.1.0-beta.11...v0.1.0-beta.12

Sage Plus v0.1.0-beta.11

Full Changelog: v0.1.0-beta.10...v0.1.0-beta.11

Sage Plus v0.1.0-beta.10

What's Changed

• Add opt-in timsTOF MS1 denoising with dnoise-core 0.5.0 by @pgarrett-scripps in #38
• Beta 10: remove --migrate-modifications by @pgarrett-scripps in #40
• Pin CI runner images to ubuntu-24.04 and windows-2025 by @pgarrett-scripps in #45
• Beta 10: remove the sage-mcp server by @pgarrett-scripps in #39
• Prefer isotope 0 on exact hyperscore ties by @pgarrett-scripps in #41
• Make cloud storage an optional Cargo feature by @pgarrett-scripps in #43
• Fit the discriminant around constant columns and explain fallbacks by @pgarrett-scripps in #44
• Add a fast-release build profile for local experiments by @pgarrett-scripps in #46
• Document searching crosslinker monolinks as mass offsets by @pgarrett-scripps in #47
• Reject Sage Plus-only symbol-key modification extensions by @pgarrett-scripps in #48
• Add a shared path for sidecar output files by @pgarrett-scripps in #49
• Add a per-spectrum mass-offset scoring hook by @pgarrett-scripps in #42

Full Changelog: v0.1.0-beta.9...v0.1.0-beta.10

Sage Plus v0.1.0-beta.9

What's Changed

• Fit RT and mobility models with a standardized ridge solve (Beta 9) by @pgarrett-scripps in #33
• Beta 9: nonlinear RT alignment by default, search-time mass recalibration, and z-dot ions by @pgarrett-scripps in #34
• Optimize test builds so CI tests run in seconds by @pgarrett-scripps in #35
• Move vendored filemanager to parquet 59 to drop thrift by @pgarrett-scripps in #36
• Release Sage Plus v0.1.0-beta.9 by @pgarrett-scripps in #37

Full Changelog: v0.1.0-beta.8...v0.1.0-beta.9

Sage Plus v0.1.0-beta.8

What's Changed

• Cache Rust builds in CI and run release checks alongside builds by @pgarrett-scripps in #30
• Release Sage Plus v0.1.0-beta.8 with review fixes, picked protein-group FDR, and motif sites by @pgarrett-scripps in #31
• Reuse prefilter spectra in the search (Beta 8) by @pgarrett-scripps in #32

Full Changelog: v0.1.0-beta.7...v0.1.0-beta.8

Sage Plus v0.1.0-beta.7

What's Changed

• Refresh Sage Plus paper for the Beta 6 release by @pgarrett-scripps in #28
• Prepare Sage Plus v0.1.0-beta.7 by @pgarrett-scripps in #29

Full Changelog: v0.1.0-beta.6...v0.1.0-beta.7