Spectronaut® 20

[Update 20.3.251119.92449] – Release date: November 19, 2025

• Added a more powerful multistep workflow for directDIA parallelization in HPC and cloud. Contact support for more information.
• Fixed issue in v20.2 where directDIA parallelization in HPC or cloud could lead to significantly different identifications.
• Fixed an issue which prevented changing of some library generation settings in Linux.
• Fixed a rare inconsistency in score normalization when loading an analysis from SNE file, introduced in v20.2.
• Fixed issue with processing of some diagonalPASEF data, introduced with v20.2.
• Fixed rendering issue with sensitivity plot in SN post-analysis.
• Added an option – skip-library-generation for lg pipeline to generate only search archives.
• Added support for library generation from Proteome Discoverer 4.0 results.
• Added the option to perform semi-specific directDIA search with full enumeration (as in v19) or smart enumeration which is faster and default.
• Added the possibility to add Gene Annotation to the experiment from a .gaf file in the command line invocation.
• Added the possibility to import the GO Ontology into Spectronaut from the command line.
• Added Lactylation modification to the modification repository.

[Update 20.2.250922.92449] – Release date: September 22, 2025

• Improved stability of run-level protein FDR in mixed workflow scenarios (label-free + labelled/Spike-In).
• Further improved robustness of FDR control across a variety of challenging scenarios.
• Improvement in protein identification (+4% on average) for timsTOF and Orbitrap Astral across a variety of biological datasets (n = 35 datasets).
• Fixed “process cannot access file” error during PSAR file generation in directDIA with library extension from PSAR in CMD or pipeline mode.
• Changed behavior on “missing modification definition” to abort the pipeline rather then removing them from the search.
• Improved error handling on searches that yield no identifications (empty raw files).
• Fixed issue that left libraries imported from external sources (like MSFragger) not being compatible with SN PTM-localization algorithm.
• Fixed rare issue with duplicated protein-groups when using “All Matching Proteins” inference strategy.
• Fixed “Use All MS-Level Quantities” was not applied to PTM level regulation analysis.
• Improved traceability of IDPicker algorithm.
• Fixed issue in global cScore normalization that could cause large drops in identifications.
• Fixed incorrect readout for “max fill-time reached” for Astral instruments.
• Fixed parsing errors during library generation when multiple modifications occupied the same site.
• Fixed a memory leak in Kuiper (used in unspecific searches or PTM probing searches).
• Fixed issue in global cScore normalization that could cause large drops in identifications.
• Improved memory GUI clean-up when closing windows.
• Added warning to user when application is almost out of GUI handles.
• Fixed incorrect summarizing the number of errors in the Analysis Log.
• Fixed issue leading to non-deterministic results when experiment analysed multiple times on the same computer.
• Fixed issue where negative modification masses (loss) could crash MS2 indexing.
• Fixed issue of potential race condition in access to enzyme database file when multiple instances of Spectronaut started at the same time.
• Fixed issue of empty Analysis Log for manageSNE command on Linux.

[Update 20.1.250624.92449] – Release date: June 24, 2025

• Added option for Grouped Peptide FDR based on “Protein Evidence” FASTA file annotation
• Fixed edge-case in FASTA import checks for duplicated protein accessions
• Added option to export report in Apache Parquet format in Pipeline Mode
• Added option to export modification enrichment plot PDF file in command line mode
• Fixed issue when default PTM-Probing modification was not available in the Modification Repository
• Added option to show count of all applicable Precursors in “Detected Modifications” post analysis plot
• Fixed a memory leak during NN-Model inference that could cause a hard-crash during directDIA search
• Fixed issue with software activation related to Linux and mounted BGS license location
• Fixed rendering issue in peptide motif plot that made “Q” look like “O”

[Minor Update 20.0.250606.92449] – Release date: June 06, 2025

• Fixed startup issues with HTRMS Converter due to missing packages