Spectronaut^® 21

[Hot-Fix 21.1.260825.94842] – Release date: August 25, 2026

•  Fixed various issues with Pivot report, introduced in SN21.0 and SN21.1

[Update 21.1.260820.94842] – Release date: August 20, 2026

• Fixed issue with channel overlapping fragment removal in some edge cases when labels are searched as variable modifications
• Fixed rare edge-case in Pulsar machine learning that could cause ML to fail or drop in sensitivity
• Added Precursor_Filtering_Fraction field for JSON settings
• Fixed a bug in the report where some proteins were not correctly annotated as “single hit”
• Fixed results reproducibility issues for the parallelized workflow for different batch sizes
• Fixed potential race-condition on –setTemp argument if multiple CMD experiments are started in parallel
• Fixed issue of freezing report export in Parquet format in Pipeline Perspective
• Fixed issue where iRT-Kit peptides added via FASTA file in directDIA were missing from report
• Added per-channel protein qvalues for plexDIA experiments and corresponding report columns
• Changed “Multi Channel Qvalue Filter -> Channel Qvalue” to now also apply to new per-channel protein qvalues
• Fixed issue with shifting rows (missing cells) in pivot report from “Method Evaluation” searches
• Fixed crash with c-terminal variable modification (terminus specificity) in combination with semi-specific or un-specific searches
• Improved memory handling during directDIA pipeline, reducing several memory spike instances during analysis

[NOTE]: This update is expected to introduce a random variation to the results with a median change of +/- 0.5% in precursor and protein ids.

[Hotfix 21.0.260609.94842] – Release date: June 09, 2026

• Fixed issue were in some command line situations, the floating session token would not be properly released on close
• Fixed rendering issue were PTM location in protein coverage plot was shifted by one position
• Fixed connectivity issue to software update service
• Fixed missing HTRMS Converter from SN21 installer

[Update 21.0.260602.94842] – Release date: June 02, 2026

1. Powered by advanced ML scoring and AI models

• 10% more protein groups on average
• 11% more immunopeptides on average
• Next gen AI models can accurately predict unseen PTMs
• Improved AI predictions for both tryptic and unspecific peptides

2. Improved Computational Performance

• Up to 30% faster merging steps when parallelizing
• 10% faster directDIA for immunopeptidomics (class I and II)
• 15% faster directDIA for timsTOF on average
• 50% smaller SNE file size when saving with XIC
• New directDIA workflow that randomly sub-selects samples for library gen

3. Improved PTM processes and reporting

• Improved PTM site localization leads to higher quality data
• Added option to collapse PTM site report by protein group
• Further improvements in site stoichiometry calculations
• New PTM site specific statistics and visualizations in post-analysis

4. Changes in Analysis Settings and Reporting

• Simplified identification settings for directDIA; default behavior remains same
• Simplified mass tolerance settings for directDIA and library generation
• New option to group peptides by In-Source Fragmentation events in the tree view
• Added summary for identifications per channel (e.g. SILAC experiment)
• Added option to automatically sub-sample runs during directDIA to increase analysis throughput
• Added setting to turn off parallelization of AI inference as in rare cases it causes CPU deadlock
• Reorganized some global settings into more appropriate categories
• Added Calibration Carry-over and Profile Strategy options to directDIA settings

5. Bug fixes and other improvements

• Fixed issue where some peptides were incorrectly labelled with UNKNOWN proteotypicity assignment
• Fixed issue where the reference condition in the condition setup could not be un-selected
• Fixed issue where library export to text based format, from the library perspective, could stall the software
• Fixed issue where using R.Attributes report column could cause an incorrect cell alignment in the resulting export table
• Fixed issue with diagonalPASEF reprocessing warning message in the UI would never disappear
• Fixed issue with manual peak integration sometimes not re-scoring the peak properly
• Fixed issue where changing temporary storage path while an analysis is running would break that analysis
• Fixed several issues related to Spectronaut Uninstaller
• Fixed issue where the user could trigger a experiment post-analysis refresh while a report export process was running
• Fixed an issue where 2 variable modifications with a combined delta-mass of 0 would cause a peptide to be treated as non-modified
• Improved error handling for experiments with individual runs that have 0 identifications