This year, ASMS is hosting a new workshop on MS software. The workshop will be held on Monday, June 4th from 5.45 pm to 7 pm in Room 8, and will be hosted by me and the superbly excellent Magnus Palmblad (LUMC, Leiden, NL).

This workshop is aimed at the many ASMS members who write their own software to control mass spectrometers or process mass spectrometry data – and those who might want to.

Mass spectrometers are highly complex systems that can shine the light of knowledge onto important problems in many areas. Advances in mass spectrometry instrumentation have led to startling improvements in performance. But, these new amazing powers of mass spectrometry would be unusable if it wasn’t for the software that is available to control the instruments and make sense of the data.

The software available for commercial mass spectrometers is remarkable. But, as the quantity and diversity of data that can be recorded, and the density of information in that data grows ever larger, in ever more complex mass spectrometry experiments, there is a continuous drive for new algorithms and bespoke software to process that data and find the right information. Consequently, there are many researchers who develop their own mass spectrometry software, and many more who might want to either collaborate with someone who can help develop a software solution to their problem or learn how to start writing their own software.

So, as a community, what do we do? What problems are we trying to solve? Have they been addressed before? What languages and platforms are we using and why? What file formats are easier or harder to work with, and which do we like the best? How can we make what we do most useful to others? Is there sufficient interest to consider requesting to become an interest group?

There are other interest groups in the ASMS where software plays a vital part in their specific applications (e.g. FTMS, Top-down and Bioinformatics). The aim of this workshop is not to duplicate any of the core interests of these groups. Instead, it is designed to provide a home for the many of us who develop MS software, who don’t have a home yet, or who stretch across multiple applications.

This year we want to look at MS data-formats, with a key focus on how to read/write them from within different languages. We have the following draft structure for the workshop:

• 1745 – 1750 Welcome and short introductions
• 1750 – 1800 Community polls – What languages are people using, what formats, what instruments and applications, which users?
• 1800 – 1845 Data formats – How to read/write them from within different languages, how these methods scale with data size, and what the limitations and caveats in the different formats are? The discussion will be kicked off with a series of short presentations providing a summary of common formats and development platforms, including:
  • Luis Mendoza, Institute for Systems Biology (mzML)
  • Stefan Schulze, University of Pennsylvania, (pymzML)
  • Mathias Wilhelm, Technical University of Munich (mz5 & binary vs XML)
  • David Kilgour, Nottingham Trent University (LabVIEW and reading MS data formats)
  • Greg Blakney, NHMFL (LabWindows & FTICR)
• 1845 – 1855 Plans for next year – e.g., focus on languages in use, ASMS forum?
• 1855 – 1900 Closing summary
• 1901 IF hungry THEN GOTO dinner ELSE GOTO pub