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Tue, 02 may 2017 17:30:15 +0200

MassChroQ 2.2.1 Black Caiman

The MassChroQ version 2.2.1 called "Black Caiman" is now available. This version brings natural isotope support to MassChroQ and a new matching algorithm. It requires less memory while computing faster. The natural isotope support brings more reliability to the results while decreasing the number of missing values.

MassChroQ homepage

Tue, 04 Apr 2017 10:39:15 +0200

X!TandemPipeline publication (JPR 2017)

Atelier PAPPSO - "Les outils bioinformatiques d'analyse des données de protéomique développés par la plateforme PAPPSO"

La plateforme PAPPSO organise du 21 au 24 novembre un atelier sur les outils bioinfo qu'elle a développés pour la protéomique.

Ci-joint la plaquette pour plus d'info.

Pré-inscription par envoi d'un mail à pappso-inscriptions@listes.inra.fr en indiquant votre nom et celui de votre laboratoire avant le 30 octobre.

Les détails de la formation sont disponibles sur le flyer a l'adresse suivante http://pappso.inra.fr/documents/plaquette-atelier-PAPPSO.pdf

Mon, 19 Sept 2016 12:00:00 +0200

X!TandemPipeline

a new version of X!TandemPipeline is available at :
http://pappso.inra.fr/bioinfo/xtandempipeline/
This is the version 3.4.0 named "Elastine Durcie".

The changes compared to previous stable version are :

  • Computation of the PAI as described in the original article (Rappsilber et al. 2002).
  • New spreadsheet reports containing more informations about original MS samples, parameter used, software versions...
  • Updated documentation.
  • New support of pepXML as input format, so X!TandemPipeline is now able to import identification data from PeptideProphet, cometMS or all other search engine compatible with pepXML.

Mon, 11 Jul 2016 15:24:20 +0200

MassChroQ 2.1.4

a new version of MassChroQ is available at :
http://pappso.inra.fr/bioinfo/masschroq/
This is the version 2.1.4 named "Yacare Caiman".

The changes compared to previous stable version are :

  • Multithread support : MassChroQ can extract and quantify XICs in parallel using the number of core determined by the user, up to the maximum capacity of your processor. This speeds up dramatically the quantification process depending on your hardware.
  • MAJOR BUG FIX : the parameter ""maxmin half edge" was not taken into account in previous release (bug reported by Samuel Granjeaud).
  • Better error messages delivered to the user to explain XML syntax error, missing files, permission problems ...

Fri, 27 Nov 2015 09:48:58 +0100

software update for Debian Jessie and Ubuntu

proteomic sotfware tools developped by PAPPSO are available in a Debian repository.
This works more or less as an "appstore".
This repository is now available and maintained for latest Linux distributions :

Thu, 10 Sep 2015 22:32:02 +0200

X!TandemPipeline 3.3.4

a new version of X!TandemPipeline is available at :
http://pappso.inra.fr/bioinfo/xtandempipeline/
This is the version 3.3.4 named "Myosine Bodybuild\E9e".

The changes compared to previous stable version are :

  • CRITICAL BUG FIX (introduced in 3.3.1) in the tabulated output for combine and individual mode (ODS or TSV report) : "peptides" and "peptide pos" displayed valid and not valid peptides.
  • CRITICAL BUG FIX in the MassChroQML output (introduced in 3.3.1) : the output contained valid and not valid peptides.
  • Experimental support for the pepXML format used by the TPP (Trans Proteomic Pipeline) and the Comet MS identification engine.
  • More details available in the "X!TandemPipeline informations" of the ODS report for each MSrun : number of assigned spectrums, number of MS1, MSn.

Fri, 06 Mar 2015 09:35:47 +0100

X!TandemPipeline 3.3.3

a new version of X!TandemPipeline is available at :
http://pappso.inra.fr/bioinfo/xtandempipeline/
This is the version 3.3.3 named "Myosine Anabolis\E9e".

The changes compared to previous stable version are :

  • bug fix concerning the expert spreadsheet output : the peptide_pos tab now displays positions of all peptides of all proteins, not just the first one of each subgroup.
  • new XML parser : this new version gives more helpfull messages in case of error reading XML files (X!Tandem results or others)
  • new support for high performance cluster throught HTCondor (this allows to launch batch analysis of X!Tandem and watch progression in the cluster)

Mon, 24 Nov 2014 13:35:02 +0100

X!TandemPipeline 3.3.2

a new version of X!TandemPipeline is available at :
http://pappso.inra.fr/bioinfo/xtandempipeline/
This is the version 3.3.2 named "Myosine Charg\E9e".

The changes compared to previous stable version are :

  • bug concerning the PAI computation on samples is fixed and the emPAI is now also computed
  • Internal modifications for better performances with less memory usage
  • Full X!Tandem SLEDGEHAMMER (2013.09.01) parameters support
  • Latest X!Tandem parameters documentation included
  • Spreadsheet output files has been completely rewritten to display more informations
  • lots of user interface bug fixed
  • new documentation

Tue, 21 Oct 2014 10:40:59 +0200

PAPPSO's Debian package repository

Today, we are launching our new Debian package repository. You will find more informations here :

http://pappso.inra.fr/bioinfo/install_ppa_debian.php

and for Ubuntu :

http://pappso.inra.fr/bioinfo/install_ppa_ubuntu.php

This repository (similar to an "app store") is maintained by PAPPSO. You will therefore find all our software :

MassChroQ, X!TandemPipeline, DenovoPipeline, FastaManager, Beads...

but also all software that we depends on :

X!Tandem, pepnovo

By adding this repository to your Debian box, you'll be prompted automatically for new updates and third party software are automatically installed and updated too.

Thanks to Filippo Rusconi and his efforts to build Debian packages in the proteomics field, our repository contains also other most valuable software pieces backported for Debian Wheezy :

OpenMS, Proteowizard, R proteomic modules, massXpert.

Thu, 17 Nov 2013 10:28:55 +0200

MassChroQ: new release version 2.0.1

Version 2.0.1 of MassChroQ, is a minor update of the "Spectacled Caiman". What is new in this version?

  • MassChroQ Studio
  • MassChroQ Studio now takes into account peptide isotopes from the MassChroqML file

  • several bug fixed
    • XML generation of the spike filter in MassChroQ studio fixed
    • MS2 alignement don't crash when there is no common peptides between two runs

The new release version can be downloaded from the MassChroQ download page .

Mon, 06 May 2013 14:30:05 +0200

MassChroQ: new release version 2.0

Version 2.0 of MassChroQ, called "Spectacled Caiman" is now released. What is new in this version?

  • MassChroQ Studio
  • This is the main novelty in MassChroQ. MassChroQ Studio is a graphical, user friendly tool, allowing to load runs or masschroqML files and to perform XIC extraction, filtering, detection and alignment on them. The results of these operations can be instantly visualized on graphical plots. The goal of the Studio is to help the user find the masschroqML parameters that best fit his data and experiment. The final parameters can be exported into masschroqML format, the user has only to integrate them in his masschroqML file.

  • MassChroQ Graphical User Interface (GUI)
  • Another novelty in MassChroQ is the MassChroQ GUI , a simple graphical interface that allows the user to launch masschroq graphically, without having to do strange things on the command-line. A graphical console allows to see the runtime messages of MassChroQ.

  • The .time and .trace alignment files
  • In the masschroq core module, we have added the possibility for the user to decide whether he wants to load previous .time files or not, and if yes to directly indicate the directory where to find these files. This way, one can use previous alignment results without having to repeat the alignment. In the same way, the user has to indicate in the alignment methods the directory on disk where to put the .time and .trace alignment files if he wants them. If no directory is specified, these files will not be written to disk by default. In previous versions of MassChroQ the .time files were always loaded from the current directory if any, and they were always written to disk in the current directory. This implicit behavior could easily induce errors. Indeed, the user had to be careful and to remember to delete the .time files that he did not wanted to be loaded. He does not have to delete anything now.

    As a consequence, the masschroqML schema has changed in MassChroQ, the current schema version being 2.0 (the same version number as MassChroQ). Older masschroqML files stay functional with the new schema, but new masschroqML files containing the .time directories attributes, will not work with older schema versions.

The new release version can be downloaded from the MassChroQ download page .

Wed, 03 Oct 2012 14:30:05 +0200

X!TandemPipeline: new release version 3.3.0

Version 3.3.0 of X!TandemPipeline, called "Myosine Rachitique" is now released. This version correct problems of grouping on very large dataset and enhanced the quickness of this steps.

If you have very large dataset, we recommend to reload xtandem results to gain benefit of this patch.

This new release will be automatically updated, but it can also be retrieved at this address .

Thu, 07 Jun 2012 13:39:23 +0100

X!TandemPipeline: new release version 3.2.0

Version 3.2.0 of X!TandemPipeline, called "Tubuline Squelletique" is now released. This version adds:

  • Support for new identification results: Mascot result (.dat format). This compatibility uses mascotdatfile library . Processing, filtering and visualization of Mascot results are similar to XTandem ones, except for the information that need protein sequences like PAI, coverage, ...
  • Correction and improvement of FDR calculation using reverse option of X!Tandem, or decoy option of Mascot.
This new release will be automatically updated, but it can also be retrieved at this address .

Thu, 08 Mar 2012 14:50:23 +0100

MassChroQ: new release version 1.2

Version 1.2 of MassChroQ, called "Longteeth Crocklet" is now released. What is new in this version?

  • The peak post-matching feature : before version 1.2 peak matching in MassChroQ was performed peak by peak during quantification, by matching peptide retention times (MS/MS level retention times) to the peak's retention time interval (MS level retention time). However, a flaw in this method is that sometimes the peptide retention times (MS/MS) are not necessarily close to the peak's retention time interval (MS). This can cause match failure of relevant peaks. The peak post-matching mode adds a second peak matching pass at the end of the quantification of each group of MS-runs. This second peak matching pass is based on the retention times (MS level) of the corresponding peaks matched during the first pass. This allows the matching of some previously unmatched peptides. The peak post-matching mode is recommended only in high resolution experiments, as it can lead to mismatched background noise peaks in low resolution ones. See the manual for more details.
  • The comparison result file : the tsv result files produced by MassChroQ are well suited for automatic statistical analysis in external tools, like the R software. But they are not well suited for simple manual or visual overview or comparison purposes. Therefore, in version 1.2, we have added a new type of tsv result file, the comparison result file, which is well suited for immediate visual comparison of results and simple manual statistical analysis on them. The comparison type of file is automatically generated with the other old tsv result files.
  • The masschroqML schema has changed, the current schema version being 1.2 (the same version number as MassChroQ). Older masschroqML files stay functional with the new schema, but new masschroqML files (containing the post matching feature for example) will not work with older schema and MassChroQ versions. This new schema is automatically installed with this new version.
The new release version can be downloaded from the MassChroQ download page .

Mon, 06 Feb 2012 12:32:55 +0200

Database Manager: new release version 2.0

This release adds the possibility to manage multiple repositories of databases. Moreover, the repository could be on remote access by Webdav protocol. This new release will be automatically updated, but it can also be retrieved at this address .

Thu, 26 Jan 2012 14:30:23 +0100

X!TandemPipeline: new release version 3.1.5

Version 3.1.5 of X!TandemPipeline, called "Kératine Moustachue" is now released. Phosphopeptide spectra now show phosphorylation loss residues. ETD spectra detection has been improved. This new release will be automatically updated, but it can also be retrieved at this address .

Wed, 25 Jan 2012 13:20:23 +0100

X!TandemPipeline: new release version 3.1.4

Version 3.1.4 of X!TandemPipeline, called "Kératine Poilue" is now released. ETD spectra can be visualized with correct c/z ion series. This new release will be automatically updated, but it can also be retrieved at this address .

Mon, 07 Nov 2011 15:20:23 +0100

MassChroQ: new release version 1.1

Version 1.1 of MassChroQ, called "Speedy Crocklet" is now released. What is new in this version?

  • It is much faster. It takes no more than 3 minutes to fully analyse 1Go of profile mzXML data and only a few seconds for 1Go of centroid ones.
  • It is much lighter. At most 400 Mo of RAM (Random Access Memory) are used by MassChroQ. In comparison, in previous versions the RAM usage size was equivalent to the size of the MS-run being analysed, which could be up to 1.5 Go. As a consequence, your personal computer stays fully functional during MassChroQ analysis.
  • It uses much less disk space. The maximum disk space used by MassChroQ is equal to the size of the biggest MS-run of your analysis. This version needs to duplicate on disk only the MS-run being analysed, this disk space being automatically freed when the analysis of the MS-run is finished. In comparison, previous versions needed a disk space size equal to the sum of all the MS-runs being analysed.
The new release version can be Downloaded from the MassChroQ download page .

Mon, 17 Oct 2011 17:28:55 +0200