Improved Peptide-Identity-Propagation (Match-between-runs) in FlashLFQ.
FlashLFQ now provides FDR control for PIP transfers, as described in this preprint: https://www.biorxiv.org/content/10.1101/2024.11.15.623880v1. This results in more confident PIP transfers and better quantification.
Other changes:
- Allows for users to include peptide-level results from MetaMorpheus searches. This enables the reported peptides to be filtered based on peptide-level FDR.
- Allows users to filter based on PEP Q-Value for MetaMorpheus search results. This generally increases the number of peptides/proteins that are quantified.
Requires .NET 8.0, which can be downloaded at the following links.
* Windows: https://dotnet.microsoft.com/en-us/download/dotnet/thank-you/sdk-8.0.401-windows-x64-installer
* macOS, x64 Intel processor: https://dotnet.microsoft.com/en-us/download/dotnet/thank-you/sdk-8.0.401-macos-x64-installer
* macOS, ARM Apple Silicon processor: https://dotnet.microsoft.com/en-us/download/dotnet/thank-you/sdk-8.0.401-macos-arm64-installer
* Linux: https://learn.microsoft.com/dotnet/core/install/linux?WT.mc_id=dotnet-35129-website