NOTE: this and the paper are now in subversion in /svn/papers/epuryear Please use that copy.

Enhancing the Mass Spectrometry I/O Framework

Abstract

Discuss how there are still many mass spec data formats in use, as well as the need for an mzXML I/O module.

Keywords

Mass Spectrometry, high performance, XML, mzXML, libxml2

1 Introduction

Discuss MSIOP as it was before this summer.

Discuss mzXML and how it is an up and coming standard.

2 Requirements

Handle mzXML I/O

Speed in peaks/s(?)

C language

SWIG wrapper for other languages

3 Use cases

Pai using this(?)

Carol’s people (?)

Example using spectralComparison

Kevin’s spectralMatch

4 Architecture

In-depth info on current (updated) MSIOP infrastructure

5 Implementation

C language

libxml2

Shared libraries

SWIG wrappers

6 Performance results

Accuracy

Speed for I/O and traversing linkedlists and structures

Memory use

7 Conclusion

Say how cool it is

8 Acknowledgements

IBG

NSF

REU

9 References

Drew, Kevin; Angulo, David; Schilling, Alex; Freeman, Tim. Mass Spectra Analysis on the Illinois Biogrid. Proceedings of 2004 Midwest Software Engineering Conference, Chicago.

Puryear, Eric; Angulo, David; Drew, Kevin; Schilling, Alex; von Laszewski, Gregor. Developing a Distributed and Scalable Foundation for Mass Spectrometry Data. DePaul^? University Tech Report. April 2005.

Steele Adam, Angulo, David S. The Illinois BioGrid^?: A Prototype for Industry-Academe Collaboration. Proceedings of 2003 Midwest Software Engineering Conference, Chicago.