1.1.0

• The Bayesian protein quantification algorithm now includes an intensity-dependent uncertainty estimation, a new FDR calculation, and a null hypothesis width that scales with uncertainty
• The match-between-runs scoring has been revamped and the MBR score is also reported for each peak in the peaks output file

1.0.4

• This is a release to test automatic uploading of the latest version of FlashLFQ to Docker Hub. No changes since release 1.0.3.

1.0.3

• Fixed a rare crash that occurred in the Bayesian protein quantification when multiple PSM files were input where the same peptide in different PSM files had different annotated proteins
• FlashLFQ is now available as a Docker container on Docker Hub
• Re-release of v1.0.3 because of missing command-line version

1.0.2

• Fixed a bug where some parameters were not passed correctly into FlashLFQ

1.0.1

• Fixed a crash in Linux resulting from a build error in the .NET Core command-line version of FlashLFQ
• Fixed a bug where absolute file paths in quotes were not passed correctly in Linux

1.0.0

• A new Bayesian fold-change analysis has been added. It estimates each protein's fold change and performs a null hypothesis significance test with either a) an emperical null hypothesis ("fold-change cutoff") estimated from the data or b) a user-defined null hypothesis
• The GUI has been completely revamped
• A Wiki has been added with extensive documentation of each of FlashLFQ's settings and functions
• A Vignette has been added so you can try all this neat new stuff out!
• FlashLFQ no longer uses MSFileReader to read Thermo .raw files. Instead, Thermo's new RawFileReader software is included in FlashLFQ. You just need to accept Thermo's licence terms to use it
• Match-between-runs is generally improved (more specific and more sensitive). It now uses the Experimental Design to improve the quality of matching
• Requiring the observation of an MS/MS identification for a protein in a condition is now optional, under the advanced settings. It is disabled by default

0.1.112

• The experimental design file now is read in even if normalization is unchecked. This affects what peptides are allowed to be matched between conditions. For a peptide to be matched to a file, at least one MS/MS-identified peptide from the parent protein must be identified in the condition. This will be optionally disabled in the next version

0.1.111

• Fixed a crash in match-between-runs
• Added more error reporting popup windows in the GUI

0.1.110

• Fixed a crash in the new match-between-runs when two files have no IDs in common
• Fixed a crash in the command-line version that sometimes occurred, due a math library missing
• A .NET Core version is out. Try FlashLFQ on Linux!

0.1.109

• Match-between-runs has been completely revamped to be more RAM-efficient. Additional improvements to MBR quantification quality are planned
• Peptide intensity summed by base sequence output has been removed
• An error report is generated upon a crash
• Various minor bugfixes/crash fixes