Hands-on Tutorial

All attendees are welcome to participate in a hands-on tutorial offered Friday afternoon, 3:30-5:30 pm.

There is no additional charge to participate.

Superior Routes to mzML for Bruker timsTOF and SCIEX TripleTOF in Fast Photochemical Oxidation of Proteins 

Presented by David Tabb (GenNext Technologies)

What Attendees Need to Download in advance & Bring to the Tutorial

Files for advance download (before you travel) are strongly recommended. The files are for attendees only. Instructions for download via FTP will be sent from to registered attendees.

Bring Your Own Laptop with special files downloaded AND set-up with:

  • The demonstration will employ software to be installed on Microsoft Windows;
  • Examining output files will benefit from a good text editor like NotePad++ ( 
  • At least 10 GB of free hard disk space, if possible. 
  • 64-bit Java runtime installed.  If you need to install, this URL should work:

Please make sure your battery is fully charged as there are very limited power outlets in the room.

This optional tutorial is open to all attendees. 

About the Hands-on Tutorial

ProteoWizard msConvert has become ubiquitous in the role of generating peak-picked mzML files from raw LC-MS/MS data since its initial publication in 2008.  Contemporary QqTOF instruments from Bruker and SCIEX, however, can challenge ProteoWizard in three key aspects: ion mobility separation, peak-picking, and precursor ion charge determination. Fast photochemical oxidation of proteins (FPOP) places considerable demands on identification software as peptides may be oxidized at almost any amino acid residue, and localization of these PTMs to particular amino acids is key to the resolution of this technique. This workshop will illustrate the use of TIMSCONVERT for Bruker and SCIEX MS Data Converter for SCIEX LC-MS/MS FPOP experiments, investigating the mzMLs they create and the identifications they yield. The tutorial will also demonstrate analysis of Thermo RAW data for FPOP experiments using a standard ProteoWizard msConvert workflow.