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README.md

Current Version

Download from GitHub:

Docker Image

About

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.

Requirements

The command-line version of FlashLFQ is cross-platform (Windows, macOS, or Linux). The GUI is Windows-only.

.NET Core 3.1 is required for both the command-line and GUI version:

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

Download

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.

Input

  • Tab-separated text file of MS/MS identifications (.tsv, .psmtsv., .txt)
  • One or more bottom-up mass spectra files. Supported formats are .raw or .mzML file formats on Windows, or .mzML format on Linux/OSX. You can convert other formats to .mzML using MSConvert.

Usage

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).

Tutorial

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.

Help

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.

Development Status

To do: 
Intensity imputation for missing values

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Ultra-fast label-free quantification algorithm for mass-spectrometry proteomics

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