v0.9.1

What's Changed

• Rework internal crate dependency hierarchy
• Use cloudpath for configuration file path and fasta file (e.g. can be S3 paths), removing the need for local files or storage

Full Changelog: v0.9.0...v0.9.1

v0.9.0

What's Changed

• Fix sage quant output description by @lgatto in #47
• Merge support for non-specific digest, N-terminal enzymes (#37) by @lazear in #40

Full Changelog: v0.8.1...v0.9.0

v0.8.1

What's Changed

• add quant.tmt_level configuration option that enables MS2 (or MSn) TMT quantitation

New Contributors

• @lgatto made their first contribution in #42

Full Changelog: v0.8.0...v0.8.1

v0.8.0

What's Changed

• Corrected a comma in the json example by @hbarsnes in #38
• Rework modifications by @lazear in #39
• Support for protein N-terminal ('['), C-terminal (']') as well as peptide C-terminal ('$') modifications
• Support for k-combinations of variable modifications. This can be specified with the database.max_variable_mods parameter

New Contributors

• @hbarsnes made their first contribution in #38

Full Changelog: v0.7.1...v0.8.0

v0.7.1

What's Changed

• Add procps to Docker image by @wfondrie in #34
• Fix bug with in silico digest: Logic around overwriting decoys with target sequences was incorrect -
  peptides shared between targets/decoys were being annotated as decoy
  peptides but assigned to non-decoy proteins. We now make sure that
  they are assigned to non-decoy proteins and also annotated as target
  sequences.

Full Changelog: v0.7.0...v0.7.1

v0.7.0

Initial support for issues related to SearchGUI integration & more general use by the broader community

Added

• Add support for user-specified enzymes to JSON file. database.enzyme.sites and database.enzyme.restrict are limited to valid amino acids
• Sage can now search MS2 spectra without annotated precursor charge states. Default behavior is to search with z=2, z=3, z=4, and then merge the PSMs for scoring

Changed

• Configuration file schema changed. peptide_min_len, peptide_max_len, missed_cleavages are now specified under database.enzyme in the JSON file
• Internal behavior of Sage was changed to enable deterministic searching
• Docker file changed from Alpine to Debian

Full Changelog: v0.6.0...v0.7.0

v0.6.0

Initial support for PeptideShaker v2.2.18-beta

Added

• Changelog
• rank column added to output file
• database.generate_decoys parameter, which turns off internal decoy generation. This enables the use of FASTA databases for SearchGUI/PeptideShaker

Changed

• Base ProForma v2 notation is used for peptide modifications, i.e. "[+304.2071]-PEPTIDEM[+15.9949]AAC[+57.0214]H"
• scannr column now contains the full nativeID/spectrum title from the mzML file, i.e. "controllerType=0 controllerNumber=1 scan=30069"
• discriminant_score column renamed to sage_discriminant_score for PeptideShaker recognition
• database.decoy_prefix JSON option changed to database.decoy_tag. This allows decoy tagging to occur anywhere within the accession: "sp|P01234_REVERSED|HUMAN"
• Output file renamed: results.pin to results.sage.tsv
• Output file renamed: quant.csv to quant.tsv
• Rename pin_paths to output_paths in results.json file

Full Changelog: v0.5.1...v0.6.0

v0.5.1

Adds support for selenocysteine and pyrrolysine amino acids

v0.5.0

• Enable direct reading/writing of files from AWS S3, using aws_sdk & tokio (sage-cloudpath crate)
• If files are read in parallel, read them in batches (currently set to num_cpus / 2) to help prevent OOM situations
• Fix bug where protein_fdr was assigned to peptide_fdr field
• Directly serialize to CSV ByteRecord, rather than going through Serde - this enables parallel serialization, which is useful for very large runs (tens of millions of spectra)
• Additional parallelization for assignment of PEP, FDR

v0.4.0

• Label-free quant has been merged into master branch. This is still an experimental feature
• Command-line arguments can be used to overwrite the configuration file
• Clean up the binary's source code src\bin\sage.rs