Proline Downloads

Proline is free to use for any purpose, and is released under Cecill open source licence (Sources available on request, migration to GitHub is ongoing).

Which Proline package should you download?

Proline is a software suite composed of required and optional components that can be installed and deployed in various ways. For simplicity and convenience we packaged these modules in different distributions depending on the intended use described below.

Once installed, the getting started page will guide you through the main features of Proline. The latest release is version 2.2 (October 2022, see Release Notes) but previous versions are still available.

Use Proline as a simple desktop application: Proline Zero

ProlineZero is an all-in-one solution running on a workstation or a laptop for a single user. This mode is based on a zip file to extract and doesn’t require any modification of the computer’s configuration nor any administrative rights (zero installation & zero footprint on the computer configuration).

Note: See more downloads for the Linux version

How to get started?

  1. Download Proline Zero
  2. Unzip it on your computer
  3. Execute the file named “Proline-Zero.exe”
  4. Read the README.md file for extra information
  5. Follow this tutorial
Proline Zero v2.2 Windows x64

Deploy a full Client-Server infrastructure: Proline Server

The Client-Server mode is made for people seeking an efficient MS data analysis infrastructure shared by multiple users. In this mode, the different components can be installed on a single server or deployed on distinct computers, each one running a single component of the software suite.

Note: once Proline Server is up and running, a client user interface is required to connect to the server. You can install the desktop application (ProlineStudio) or the web application (ProlineWeb). See more downloads

Proline Server v2.2 Archive File

More Downloads

The graphical user interfaces needed to connect to Proline Server are available in this section (different packaging, differents OS). Other packaging of Proline Server are also available here. Proline source code is available on GitHub (Contact: Christophe Bruley).

Proline GUI

The graphical user interfaces needed to connect to Proline Server are available in this section (different packaging, differents OS).

Proline GUI packages (Proline Studio, Proline Web)

Proline Studio

The rich client interface, is distributed in a Zip file that must be extracted on each client computer.

Proline Web

Proline Web is the web client interface

  • Windows Installer – Not Available: Installs the Proline Web application and optionally the MongoDB server.
  • Archive file – Not Available: Contains the Proline Web application without its requirements.

Proline Server

Proline Server distribution contains Proline Server (the server Core component, Cortex), Proline Admin (for system administration purpose) and Sequence Repository (to gather proteins information from fasta files).

Proline Server full installation packages

Proline Zero

ProlineZero is an all-in-one solution running on a workstation or a laptop for a single user. This mode is based on a zip file to extract and doesn’t require any modification of the computer’s configuration nor any administrative rights (zero installation & zero footprint on the computer configuration).

Proline Zero packages

Archive page

To download old version of the software, see the archive page.

MS Files Toolset

Proline relies on the mzDB file format for MS data processing and visualization. We thus developed a set of tools to convert instrument vendors proprietary file format into mzDB files (raw2mzDB) and to visualize MS data from mzDB files (mzScope).

List of ProFI utilities dedicated to mzDB files conversion and visualization…

RawToMzDB converter

Convert instrument vendors proprietary file format into mzDB files. This converter is required by Proline for LC-MS quantification processing since Proline uses mzDB files. Read the documentation or forum messages for more information. Version 0.9.10 is the recommanded version for Proline, more recent version are available on GitHub.

mzScope

mzScope is a simple viewer for mzDB file formats. The documentation is available in the Proline User Guide. mzScope is a desktop application supplied as a simple archive file to unzip.

Automation Toolset

For those of you using Proline on a daily basis, we have also developed tools to automate some tasks: MS-Angel can be used to define workflows involving several steps such as file conversions, MS/MS searches, search results import, validation & quantification, while mzDB-Wizard can be used to batch convert raw files and upload resulting mzDB files to the server.

List of ProFI tools to designed for data processing automation…

MS-Angel GUI

The MS-Angel Graphical User Interface can be used to define data processing workflows involving several steps such as file conversions, MS/MS searches, search results import in Proline, Proline results validation & quantification.

Important note: it is mandatory to first install the Proline Web extension (see above) to take advantage of the MS Angel tool. You can find the MS-Angel documentation here.

  • MSAngel v0.5.0 : set up data processing workflows including Proline algorithms.
    Warning: not compatible with Proline v2.0.

mzDB Wizard

This tool allows user to easily convert raw files to mzdb (for XIC quantitation) and upload them on server side. This application embed the recommended version of raw2mzdb converter. You can find the mzDB Wizard documentation here.

Sample Datasets

To help getting started with Proline, examples of MS raw data and Mascot identification result files are available to download.

Details of the ProFI Yeast-UPS1 spiked-in experiment…

Samples (2 μg of yeast cell lysate + different spiked levels of UPS1) were analyzed in triplicate by nanoLC–MS/MS on an LTQ-Orbitrap Velos mass spectrometer. For more information on samples preparation and LC-MS/MS analyses, please refer to Ramus et al., J Proteomics. 2016 Jan 30;132:51-62. doi: 10.1016/j.jprot.2015.11.011.

SAMPLERAW FileMascot dat FilemzDB File
2µg levure UPS1 100fmol- Replicat 1OEMMA121101_61b.rawF083068.datOEMMA121101_61b.mzdb
2µg levure UPS1 100fmol- Replicat 2OEMMA121101_63b.rawF083069.datOEMMA121101_63b.mzdb
2µg levure UPS1 100fmol- Replicat 3OEMMA121101_65b.rawF083070.datOEMMA121101_65b.mzdb
2µg levure UPS1 10fmol – Replicat 1OEMMA121101_36b.rawF083064.datOEMMA121101_36b.mzdb
2µg levure UPS1 10fmol – Replicat 2OEMMA121101_38b.rawF083066.datOEMMA121101_38b.mzdb
2µg levure UPS1 10fmol – Replicat 3OEMMA121101_40b.rawF083067.datOEMMA121101_40b.mzdb

Short protocol description: Peaklist were generated using the Extract_msn.exe macro provided with Xcalibur. Peaklists were submitted to Mascot database searches (version 2.5.1). ESI-TRAP was chosen as the instrument, trypsin/P as the enzyme and 2 missed cleavages were allowed. Precursor and fragment mass error tolerances were set at 5 ppm and 0.8 Da, respectively. Peptide variable modifications allowed during the search were: acetyl (Protein N-ter), oxidation (M), whereas carbamidomethyl (C) was set as fixed modification. Databases used were yeast database from UniprotKB (S_cerevisiae_ 20121108.fasta, 7798 sequences), a compiled database containing the UPS1 human sequences (48 sequences) and the corresponding reversed databases in order to calculate FDR.