FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.
This repository is for the stand-alone application of FlashLFQ. FlashLFQ is also bundled into MetaMorpheus.
The command-line version of FlashLFQ is cross-platform (Windows, macOS, or Linux). The GUI is Windows-only.
.NET 8 is required for both the command-line and GUI version: https://dotnet.microsoft.com/en-us/download/dotnet/8.0
To download FlashLFQ, go here. Click the FlashLFQ.zip file and extract the contents to a desired location on your computer.
FlashLFQ is also available as a Docker container.
Alternatively, FlashLFQ is bundled into MetaMorpheus, which can be downloaded here. MetaMorpheus is a full-featured GUI proteomics software suite that includes mass calibration, PTM discovery, search algorithms, and FlashLFQ.
- Tab-separated text file of MS/MS identifications (.tsv, .psmtsv., .txt)
- One or more bottom-up mass spectra files. Supported formats are .raw (Windows/Linux) or .mzML (Windows/Linux/macOS) file formats. You can convert other formats to .mzML using MSConvert.
- Direct use of Thermo raw files requires acceptance of a Thermo License. If you would like to process Thermo .raw data files directly, you must agree to the Thermo license. This is accomplished by creating a text file with the name "LicenseAgreements.toml" with the text below. This file should be placed in the same directory as the executable program.
HasAcceptedThermoLicence = true
FlashLFQ can be used as a command-line program or in a graphical user interface (GUI). It is also built into the MetaMorpheus GUI (see MetaMorpheus).
To get started using FlashLFQ, please try the vignette. This is a helpful tutorial that provides the necessary input (spectra files, etc.) for you to try FlashLFQ. If you want to learn more about how FlashLFQ works, please check out the Wiki.
The Wiki contains a lot of useful information including a description of FlashLFQ's settings, how to get started with our vignette, and how to interpret the results in the Bayesian quantification file. Check it out!
There are two methods to contact us. You can create a new issue on the GitHub Issues page if you are comfortable with your question being public. This helps other people, because it is likely that someone else has the same question. For private correspondance, please email mm_support at chem dot wisc dot edu.