The Data Management Plan of the facility is now available on Opidor !

PAPPSO’s Data Management Plan.

Some changes since the last announced version 0.4.50 :

• Software renamed from X!TandemPipeline to i2MassChroQ
• New user documentation HTML or PDF
• Statistic module integration MCQR
• i2MassChroQ contains mzxmlconverter
• i2MassChroQ contains tandemwrapper

mzxmlconverter : Bruker’s TimsTOF pro MS2 spectrum conversion to mzXML

This command line tool process raw MS2 TimsTOF data to produce high quality MS2 spectrum in the standard mzXML format (useable with any other tool). Available documentation

The PAPPSO users’ scientific council will take place on May 16 and will be open to all, users of the facility or interested by its activities. This half-day of information and presentations will be available in person at IDEEV (12 route 128, 91190 Gif-sur-Yvette, Rosalind Franklin room on the first floor) or by video via the following link (https://orsay.bbb.cnrs.fr/b/lan-l7m-axe-ais)

Some changes since the last announced version 0.4.42 :

• New user manual
• Better annotated spectrum window
• MCQR integration : basic XIC analyses and computation of protein quantities
• Enhancements on the TimsTOF pro TDF parser
• New background noise removal specific to TimsTOF signal (better quantifications with MassChroQ)
• tandemwrapper.exe is included in the archive (utility to process X!Tandem identifications directly on Bruker’s directories .d)
• Bunch of GUI bug fix (thanks to Kevin ROGER kevin.roger@inserm.fr)
• Chemical formula added of peptides added to ODS output

Development headquarter : ForgeMIA gitlab

MassChroQ version 2.4.3 “Caïman à lunettes” is available.

Main features :

• Severe bug fix concerning “match between run”
• Better computation performances
• Redesigned code to handle natively timsTOF pro runs, taking into account ion mobility dimension.
• New outputs to get a peak detection quality value (see above)

Peak detection quality is reported for each XIC with these values :

aa

best quality : many MS2 fragmentation event, only one peak directly detected

a

good quality, single MS2 fragmentation event, one peak detected

ab

many MS2 fragmentation event, but more than one peak detected, the greater peak (area) is chosen, it is obviously fragmented... perhaps a hint to check for peak detection parameters

b

peak obtained by "match between run" on the mean aligned retention time

pm

peak obtained by post matching (retention times are refined using peak detected in aa, a, ab, b categories)

missed

no peak detected