DIA-NN 1.7.13 development build

Significant improvement of multiple algorithms & functionality changes, please contact by email (provided in the manual) for details on the new functionality. An updated manual describing all the new features will be available in the future.

DIA-NN 1.7.12

1. Major improvement in protein FDR calculation: DIA-NN now identifies significantly more proteins. Further, if the spectral library has been created by DIA-NN from DIA data, protein FDR is now significantly more reliable.
2. Minor improvements in peptide identification performance.
3. Flexible cleavage specificity support for in silico digests of sequence databases.
4. "Quantity.Quality" metric is now reported for each peptide-spectrum match.
5. File names without the full path to the file are now also included in the report.
6. Ability to restrict precursor charges for library-free searches using --min-pr-charge and --max-pr-charge commands.

I have received numerous feature requests since the DIA-NN 1.7.11 release, some have now been implemented, some are in the TODO list and hopefully will be included in the next version.

DIA-NN 1.7.11 development build

A bug which manifested when using the "Quantities matrices" feature has been fixed. The bug led to extra missing values in protein x sample matrices (some protein quantities were just skipped). No algorithmic changes.

DIA-NN 1.7.10 development build

• MaxLFQ-based protein quantification. We tested it on several large plasma screens an found that it performs superbly; LFQbench test results are also excellent.
• Improved protein grouping: now DIA-NN will report less protein groups in total and less proteins in each group.
• Protein group/gene group level FDR - it is recommended to filter DIA-NN reports based on this at 1-5% q-value.

Update: this version has a bug in the generation of protein "Quantities matrices", fixed in 1.7.11.

DIA-NN 1.7.9 development build

• Support for the entire UniMod modification database.
• Retention time information support for .sptxt/.msp spectral libraries.
• MS1 peak area information now saved to the report.
• Bugfix for the experimental --peak-translation mode.

DIA-NN 1.7.8 development build

Multi-tab GUI - now it's convenient to analyse multiple experiments in parallel.
Experimental support for NIST .msp and SpectraST .sptxt libraries.
Bugs affecting SILAC analysis & N-terminal modification search fixed.

DIA-NN 1.7.7 development build

• Ability to control which fragments are used for quantification (--restrict-fr command, see manual, page 4).
• Experimental option to perform cross-run normalisation of precursor quantities in intensity-dependent manner (use with caution).

DIA-NN 1.7.6 development build

Previous versions could crash when generating a spectral library from >1.5 million precursors, when the search has returned a very low number of confident identifications. This is now fixed. No algorithmic changes.

DIA-NN 1.7.5 development build

Deep learning-based spectra & RTs prediction.

Switching to using GitHub 'pre-releases' to store binaries of development builds.

DIA-NN 1.7.4

Retention times were not saved to the spectral library when analysing in library-free mode without a training library. Fixed now. However, using a training library is still highly recommended anyway.