Software:RAMP

RAMP

RAMP: Random Access Minimal Parser

C/C++ parser for mzXML (and mzData) files. The RAMP parser code is contained in the TPP source tree. RAMP is heavily used in the TPP; this allows programs to seamlessly adapt to revisions to the mzXML format, as well as handle other formats such as mzData. RAMP itself is C-language code; "cRAMP" is a C++ wrapper.

RAMP in the TPP

• MzXML2Search – RAMP
• ASAPRatio – RAMP
• Xpress – RAMP
• Libra – RAMP
• SpectraST – cRAMP
• pep3D -RAMP
• MS/MS spectrum viewer - RAMP

External Projects

• muxQuant (M. Palmblad)

Getting the software

• stable: You can also look in the latest stable/official source release, under /trans_proteomic_pipeline/src/Parsers/ramp/

• stable (svn): [http://sashimi.svn.sourceforge.net/viewvc/sashimi/tags/release_3-4-0/ 1

• Latest (bleeding edge) is in the SVN trunk: http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/src/Parsers/ramp/

History and Design Decisions

RAMP was developed at time when full XML parsing libraries (such as xerces) were heavyweight and slow, and not suited for the fast, random-access parsing of large spectral files in proteomics applications. As such, the code is string-based ASCII processing rather than true XML parsing. This unfortunately also makes RAMP fairly dependent on the whitespace in mzXML, and occasionally the order of attributes within elements.

Related projects

• JRAP-- java mzXML parser
• RAP-- earlier xerces-based mzXML parser, retired.
• X!Tandem uses a custom SAX-based parser