Can MSe or HD-MSe data be exported as MassLynx RAW files for analysis in PLGS or Progenesis QIp? - WKB44745

ENVIRONMENT

• UNIFI 1.9 SR3
• UNIFI 1.9 SR4

• MassLynx

• ProteinLynx Global Server (PLGS)

• Progenesis QI for Proteomics

• Vion IMS QToF

• Xevo G2-XS QToF

ANSWER

Neither Vion IMS-QToF, or Xevo G2-XS QToF under UNIFI control, support proteomics workflows, even if you export the data to other file formats such as MassLynx (.raw), Mascot Generic Format (MGF), or open standard file formats such as mzML.

ADDITIONAL INFORMATION

UNIFI restricts the number of peaks from a given acquisition to prevent the Oracle database from becoming unusably large. MSe proteomics acquisitions typically produce data files that contain millions of peaks. Thus, UNIFI does not support acquisition of proteomics data from Vion or XevoG2-XS. If you do acquire proteomics data, not all of the required peaks will be there after exporting to .raw format. The data is truncated. The exported files won't contain all the peaks, and analysis of the data in PLGS, Progenesis QIp, or Mascot will either fail completely or produce only partial results.