Here is the changelog since last announced 0.2.38 version :

• better XICs display
• new window to display the list of MS run identifications : access to the parameters of each identification, quality control of MSruns (assigned percentages, MS1 MS2 counts …)
• better masschroqML output, with the choice of the best MS run to use in the alignment, either automatically or manuall.
• suppor of the modified version of X!Tandem from the TPP X!Tandem TPP (used to build DIA libraries)
• new PAPPSOms++ library bringing powerfull MS filters, raw data file parsers…

Many thanks to the PAPPSO team and specially to Thomas Renne, bioinformatics apprentice, for the development of most of these new features.

Développement de nouvelles méthodes d’acquisitions de spectrométrie de masse pour l’analyse protéomique

• Niveau de qualification: BAC+2
• Date prévisionnelle de démarrage: à définir
• Durée du stage: 2 mois
• Lieu du stage: INRAE PAPPSO - 78350 Jouy en Josas
• Contact: lydie.oliveira-correia@inrae.fr

Environnement

La Plateforme d’Analyse Protéomique de Paris-Sud Ouest (PAPPSO), spécialisée dans les questions de protéomique par spectrométrie de masse, réunit deux sites complémentaires chacun orienté vers des thématiques propres : l’un situé au Moulon (Gif-sur-Yvette) expert en biologie végétale, l’autre à l’INRA de Jouy-en-Josas expert dans l’analyse d’organismes procaryotes ou eucaryotes où le stage proposé sera réalisé. PAPPSO est certifié ISO 9001 et est labélisé Infrastructure Scientifique Collective (ISC) par l’INRA et IbiSA (Infrastructure biologie santé et agronomie, label inter organisme de recherche).

Here is the changelog since last announced 0.2.36 version :

• better masschroqML export dialog with a new droplist button to choose the MS run to use as reference for the alignment and an automated algorithm to look for the best MS run reference to use.
• TPP X!Tandem modified version supports (usefull t o initiate identifications to build DIA library)
• new PAPPSOms++ library featuring optimized spectrum filters
• bug fix in masschroqML export dialog : the XIC extraction method sum or max was not taken into account

Many thanks to Marlène Davanture and Thierry Balliau for the sum/max bug report.

Here is the changelog since last announced 0.2.32 version :

• Small screen adaptation. A lift is available if the screen is too small to be able to click on OK button.
• New choice in the computation of XIC intensities. “sum” computes the sum of intensities inside the precision range. “max” will take only the maximum of intensitie.
• New screen to edit global settings (edit => settings). 2 methods to extract XICs are available. “buffered” is very fast but requires some extra space on the hard disk. “direct” is a bit slower but does not require extra space.
• Better ODS exports. new column to display mass delta in “ppm” in the “spectra” sheet.
• Modifications in “protein list” and “peptide list” windows. A new menu is available to select “valid”, “checked” and “grouped” proteins/peptides. A direct export in tabulated sheet of the view is available. Flanking Nter and Cter regions are now displayed.
• Better X!Tandem import filter to take into account “point mutation”.
• New filter “peprepro” to select valid peptides. It allows to consider peptides only if they are seen in one or more MS runs.
• Bette PROTICdbML support
• New controls to help the use of X!Tandem

Many thanks to Solenne Chardonnet, Cédric Pionneau, Valérie Briard-Bion, Julien Jardin and the PAPPSO team for their contributions.

PAPPSO is member of GDR “post translationnal modifications on bacteria”. site web GDR