FlashLFQ + PIP-ECHO

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

1.2.6

Removed extraneous white space characters from output files.

Previously, all outputs had an extra trailing '\t' character at the end of their respective headers. This update fixes that issues.

1.2.5

• Fixed a bug in the default protein quant that resulted in erroneous missing values
• Other minor bugfixes
• (Beta) Support for reading Bruker .d data

1.2.4

• Fixed a bug where Percolator PSMs could not be read in properly due a file name mismatch

1.2.3

• Reading Percolator PSMs is now faster
• File paths within the PSMs file are handled better

1.2.2

• FlashLFQ now requires .NET 6 runtime
• The comma (",") character is used to delimit proteins in Percolator input
• Fixed a crash that occurred when empty scans were present in a spectra file

1.2.1

• FlashLFQ now requires .NET 5 Runtime
• Identifications from Percolator can now be used as input to FlashLFQ

1.2.0

• Much better default (non-Bayesian) protein quantification. The default protein quant method is now median polish instead of top3
• Fixed an issue where the Docker image could not be run properly in Singularity
• Fixed a rare crash in match-between-runs

1.1.2

• This version and future versions require .NET Core 3.1 from Microsoft.

Windows: https://dotnet.microsoft.com/download/dotnet-core/thank-you/runtime-desktop-3.1.3-windows-x64-installer

Mac: https://dotnet.microsoft.com/download/dotnet-core/thank-you/runtime-3.1.3-macos-x64-installer

Linux: https://docs.microsoft.com/en-us/dotnet/core/install/linux-package-manager-ubuntu-1910

• Fixed some culture-dependent number parsing issues

1.1.1

• The Bayesian protein quantification requires a log2 fold-change cutoff that is considered uninteresting; by default, this is 0.1 but can be set to any non-negative number, including 0