Proline

An open source data integration framework and a software suite for mass spectrometry based proteomics:

  • Multiple search engines support
  • Target/decoy results validation
  • Easy datasets comparison using spectral counting
  • Efficient label-free MS quantification
  • User-friendly data visualization
  • Highly customizable results export

Features

Discover the open-source Proline software suite

Downloads

Download the latest stable release of Proline.

Support

Installation guide, user manual and training materials.

Proline Release 1.6 is available !

New validation service, PTM sites identification available for merged dataset and more than 50 bug fixes…

Features

Import & validation

identification results imported from Mascot or OMSSA search engines. Proline will capture results as as well as meta data in its datastore. Target-Decoy searches issued from protein database concatenation or from search engine decoy search are handled in the same way by Proline.

Quantitative Proteomics

Label free quantification based on spectral counting or based on signal extracted from MS1 level can be easily and efficiently achivied with Proline.

Export Validated result

All Proline results can be exported as tabulated files (support of TSV and Microsoft Excel formats). These exports are fully customizable (choice of tabs and columns). Identification results can also be exported to the Pride XML Format.

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 1.6 (january 2018) 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

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

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 upon request (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 – Coming soon: Installs the Proline Web application and optionally the MongoDB server.
  • Archive file – Coming soon: 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

  • Windows Full Installer – Coming soon: Installs Proline Server modules and optionally PostgreSQL server (for Windows OS). Require administrative rights
  • Windows Installer – Coming soon: Installs Proline Server modules (for Windows OS). PostgreSQL should already be installed, separately. No specific rights are required.
  • Archive file: Contains archives for Proline Server modules. For manual installation on Windows or Linux OS..

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.

RawToMzDB: convert Thermo raw files into mzDB files.

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.

mzScope: (version 0.5.0) Visualize MS data from mzDB files (requires Java 8).

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.

MS-Angel GUI: set up data processing workflows including Proline algorithms.

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.

mzDB Wizard: convert raw files into mzDB files and upload them on server side.

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.

SAMPLE RAW File Mascot dat File mzDB File
2µg levure UPS1 100fmol- Replicat 1 OEMMA121101_61b.raw F083068.dat OEMMA121101_61b.mzdb
2µg levure UPS1 100fmol- Replicat 2 OEMMA121101_63b.raw F083069.dat OEMMA121101_63b.mzdb
2µg levure UPS1 100fmol- Replicat 3 OEMMA121101_65b.raw F083070.dat OEMMA121101_65b.mzdb
2µg levure UPS1 10fmol – Replicat 1 OEMMA121101_36b.raw F083064.dat OEMMA121101_36b.mzdb
2µg levure UPS1 10fmol – Replicat 2 OEMMA121101_38b.raw F083066.dat OEMMA121101_38b.mzdb
2µg levure UPS1 10fmol – Replicat 3 OEMMA121101_40b.raw F083067.dat OEMMA121101_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.

Support

Getting started

Learn to use Proline and get started with Identification, Spectral count or label-free quantitation based on LC-MS signal detection. These tutorials are based on MS data and Mascot identification results that can be downloaded from this site.

Forum

If you need help regarding the installation or use of Proline, you can communicate with the members of the development team and other Proline users through the Community Forum.

Release Notes

Proline release notes provide information on the features and improvements in each new release

Version 1.6 (& Studio 1.6.1...)

  • New features in Proline Server:
    • Ptm sites identification for identification and merged RSM
    • Improve search result import performance
    • LC-MS quantitation
      • user can choose to not cross align features between groups.
      • user can choose to retain only reliable cross aligned features.
      • Generated quantitiation datasets list also subset proteins.
    • Validation
      • Add mudpit score for protein sets scoring type
      • Allow user to propagate validation parameters from parent to child datasets
    • Export Pride: fixes connexion to onolies server probel and peptide with ‘X’ in sequence correctly exported
    • Allow SC on merged Search Result if a Validation with propagate on child has been run.
    • Generate sprectrum matches: now generates “z+1″ and “z+2″ ion series depending on the instrument config
  • New features in Proline Studio 1.6.1:
    • Export Pride needed new JRE to connect to ebi site
  • New features in Proline Studio 1.6:
    • Parallel Coordinates first version
    • DataAnalyzer
      • Allow multiples joins
      • venn diagram available
      • Added adjustP column to Compute FDR Function
    • MsFile
      • Raw to mzdb conversion accessible
      • Upload mzdb files on server side (necessary for LCMS Quantitation)
      • Download of mzdb files from server locally
      • Add Working sets containing set of mzdb files to work on
    • MzScope
      • mzScope module enhanced : better isotopic prediction – MSData in profile mode display
      • First implementation of id free QC metrics
      • Display mzdb file properties (converter version, acquisition date, format version, acquisition mode, data encoding)
  • Changes in Proline Web eXtension:
    • MS-Angel
      • New features
        • Integration of the SearchGUI tool
        • Support the import of Comet results in Proline (through the creation of mzIdentML with IdConvert)
        • Support default peak picking with MsConvert
        • New panel allowing to design quantitation ratios and post-processing configuration
      • Improvements
        • GUI: better configuration checks and errors display
      • Fixes
        • Fix files monitoring errors (more tolerant, won’t affect the other tasks)
        • Fix many bugs in GUI and task execution
    • Dataset Explorer
      • New features
        • Link favorite proteins and peptides to volcano plots
        • Add identification/quantitation folders to projects tree
        • React to peptide/peptide ion selection(/deselection) in dataset/in protein
        •  Integration of Lorikeet viewer
      • Improvements
        • Add and re-organize columns in all identification tables
        • Check ratios validity when updating the experimental design
        • Improve tree items manipulation (re-ordering)
      • Fixes
        • Fix link to Uniprot
        • Minor display fixes
    • SpecLight
      • Improve the speed of XICs display and resize
      • Fix some visualization bugs
    • Heatmaps
      • Add module to PWX as a new app, accessible via Proline Web interface
      • Export data as TSV format
      • Add charts for quantitative profiles display
      • Re-arrange main layout
    • Raw File Explorer
      • Externalize view as an application accessible via the Proline Web home page

 

Previous versions

Version 1.5

  • LC-MS quantitation performance optimization and enhancement: lower memory consumption and faster quantitation processing
  • Export enhancement
    • Several bugs fixed (order of columns, MW&coverage, fix the computation of #PSMs/#Specific PSMs/#Sequences, support of decimals with comma separator)
    • Quantitative exports: keep sample order (same as specified in GUI)
    • Add some new columns: samesets/subsets accessions, gene name, PTM location on protein, number of observable peptides, observed m/z and corrected RT of each quantified ion.
  • Short services are treated separately. This prevent waiting fot connection, server browsing… when server is busy.
  • Determination of spectrum retention time
    • Update Spectrum using new Peaklist software : fixes issues in order to get RTInSeconds if no value found for Time
    • Fix a bug: RTINSECONDS was not taken into account when its value was zero

New features in Studio:

  • Add Folder in quantitation and identification tree
  • XIC dialog bug fixes and enhancement and separate simple vs advanced parameters
  • Ability to cancel server running tasks
  • DataAnalyzer
    • import CSV : automatic detection of the separator, preview of the file parsing, bug fixes when loading data from CSV
    • Enhancements for ProStar Macro : Graphical Selection of Thresholds, possibility to show Differential Proteins
    • New algorithm for Diff/join : possibility to have 2 keys and one of the keys can be a double value with tolerance.
  • Add Admin features (add/modify user; peaklist software…)
  • Raw/MzDB : Convert and/or upload on Server side
  • Bug fixes for Adjacency Matrices : memory problems, tasks not stopped
  • Observable Peptides column for validated proteins (need to potentially retrieve protein sequences)

New features in Web:

  • Set/Unset favorites in batch from table content (using table filters)
  • Clone a quantitation: open pre-filled form to launch a new quantitation
  • Utilities to copy all tables
  • Vizualize the parameters used for LFQ and post-processing
  • Fix user creation
  • Add organization folders in quantitation tree
  • Some enhancements in SpecLight XIC visualization

New features in MS-Angel:

  • Improve panel for input files
  • Add many checks for workflow validity, previous to task launching
  • Improve/fix task cancellation

New features in mzDB-Wizard:

  • New two-step opening dialog. In step 2 we can now select an existing mounting point based on the server selection done on step 1.
  • Possibility to restart failed task.
  • Check for corrupted files before running actions.
  • Add MGF export from mzdb files.
  • Task Manager : sorting is now possible ans more tasks’ details displayed.
  • User Interface changed ti be more user friendly
  • Documentation is accessible inside the application.
  • Logs: in GUI now contain date & time; Refined all messages and changed logfile names

Version 1.4

  • New global features (on server):
    • Quantitation Refine : new Abundance Summarizer method, Median Ratio Fitting
    • Filter : add Protein Set score filter
    • Export
      • Quantitation export : elution time and peptide number was wrong
      • Export Pride : explicit error when spectra are missing
    • Spectral Count : Fix error when parent identification summary was added in list of identification summaries to calculate SC for
  • New features in Studio:
    • Add a “General Settings” windows
    • Ability to view also Server Tasks Logs and to cancel user pending tasks
    • XIC Quantitation
      • experimental design : Drop Zone to automatically associated mzdb files to Identification Summaries
      • result could be refined by selecting/unselecting quantified peptides
    • New Data Analyzer, finished first integration of DAPAR (ProStar)
    • Navigation facility : added a popup option in all data tables to display complementary information. (Like adjacency matrix for a Protein, Identification data for XIC Protein Set…)
    • Enhanced Adjacency matrices : added selection of Proteins/Peptides
    • Export : change default value for ProteinSet list to export : Only validated by default
  • New features in Web:
    • Add a system for favorite entities
    • Add a tool to change sample names in batch using copy/paste from an Excel table
    • Add a tool to create a dataset on 2 or 3 levels using copy/paste from an Excel table
    • Improve information on quantitation result graphics (tooltips)
    • Add tables in quantitation viewers, replacing the protein set grouping system
    • Selection/deselection of a peptide at protein/dataset level
    • Ease the creation of the experimental design (improve drag and drop, display sample name)
    • Fix some display bugs, in particular toward tables rows filtering
  • About 50 issues closed…
  • New Tools are available in this Release
    • mzDB-Wizard: this tool allow user to easily convert raw files to mzdb (for XIC quantitation) and upload them on server side
    • MS-Angel: Provide a complex workflow, complete data visualization, real time monitoring, submission to many search engines (Mascot, OMSSA, X! Tandem: in progress).

Version 1.3

  • New global features (on server):
    • Algorithm and other operation
      • Faster datasets export
      • New service to clean up a project : remove unused identification data (Search Results or Identification Summaries put to trash or no more accessible to user, after re-validation for example)
      • New Quantitation Post-Processing options
      • Import MzIdentML result file
  • New features in Studio:
    • Allow to run “XIC” from a merged dataset. The identification summary associated to the dataset will be used as parent identification summary of quantified identification summaries.
    • XIC – experimental design : Change view to associate mzdb files to dataset
    • Simplify Mascot specific parameter in import
    • Integration of R package DAPAR(also interfaced with ProStaR)
  • About 40 issues closed…

Version 1.2

  • New global features (on server):
    • Algorithm and other operation
      • Fragment Match Generator for XTandem result.
      • FDR change : Use TD competition if rank filtering is used
      • XIC Enhancement
  • New features in Studio:
    • Menus’ reorganization (Identification and Quantitation)
    • New display of MsQueries (for a Search Result or an Identification Summary)
    • XIC: New display of experimental design and XIC parameters
    • XIC: New display of alignment map and calculating of predicted elution time
    • MzScope (mzDB file viewer) convert into MGF files, display of multi raw files, LCMS map viewer
    • Allow Fragment Match Generator to be called from both Identification & Quantitation Trees
    • Add spectra Library generation
  • New features in Web:
    • Customizable export of identification and quantification datatsets
    • Enhancement of quantification results visualization
    • Integration of Spectlight, a 3D web-viewer of mzDB files to manually check a peptide environment and its XICs over all input files
  • About 150 issues closed…

Version 1.1

  • New global features (on server):
    • Algorithm and other operation
      • Spectral Count algorithm modification: Spectral Count Weigth is based on specific PSM count instead of specific peptide count.
      • ProteinSets filtering (independently of validation)
    • Save, import and export ◦Export to PRIDE format
      • Support import of X!Tandem result file
  • New features in Studio:
    • Algorithm and other operation
      • Enhancement of data mixer: module to easily do calculations/comparisons on data.
      • Integration of a calculator: it lets you write python scripts to manipulate freely viewed data.
      • Add interface for ProteinSets filtering
    • Save, import and export
      • Customizable export of Identification dataset, or Spectral Count or XIC
      • Add interface for Export to PRIDE format
      • Add interface for import of X!Tandem result file
    • Display
      • Display MzDB Files through mzScope module (directly in Studio)
      • Enhancement of the XIC display and Spectral Count display
  • New features in Web:
    • New & improved Interface !
    • New data and chart vizualisations for quantitation stats

More Documentation

 

Database Schema

You will found here schema of the different databases used in Proline :

  • MSIdb contains all identification and quantitation results for a given project
  • LCMSdb contains maps of MS features for a given project
  • UDSdb contains information on projects, user and identification and/or quantitation experimental plan
  • PSdb contains informaion on peptides and ptms seen over all projects