Some changes since the last announced version 0.4.3 :

• Builtin TDF data reader from TimsTofPRO : X!Tandem identifications, MS2 spectrum visualization, XIC extraction
• Ion mobility ready
• Complete GUI to configure and launch MassChroQ
• Improvement of the mzIdentML reader
• Overall GUI improvements

Thanks a lot to the PAPPSO team for these improvements, especially to Thomas Renne, bioinformatics trainee, that has developped many new features.

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.

PAPPSO joined the COVID-19 Mass Spectrometry Coalition initiated by the British Mass Spectrometry Society and for which the objective is to use mass spectrometry to reduce the harm caused by thje SARS-Cov2 virus. Samples, expertises, data and protocols will be shared between mass spectrometry experts to optimize and accelerate the development of diagnostic and virus characterization and tracking.

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.