Mass Spectrometry Database Committee

More About Software Compatibility

Hewlett Packard* (Agilent) Systems

Mass spectral libraries on the Hewlett Packard DOS ChemStation and UNIX ChemSystem MSD operating systems use a similar format. These libraries consist of 6 binary files (7 in the case of the UNIX system), that reside under a library subdirectory (e.g. aafs9808.l). The key to being able to edit and change user-generated libraries lies in the fact that they all use an intermediate file format call "JCAMP" - specifically version 4.10 at present. User generated libraries can be converted into "text" files which can be read and edited with a standard text editor. Both the DOS ChemStation and UNIX ChemSystem software have macros which assist in the conversion of these libraries (i.e. read JCAMP files and convert into libraries, or the reverse - write JCAMP files from binary libraries). Some of these macros are readily available under the Parametric Retrieval menu (ChemStation), while others have to be called from the command line under DataAnalysis (ChemSystem).

Any user-generated library can be edited in this way. While some changes (e.g. changing the drug name can be done through existing menus, other changes, such as changing the molecular weight or editing ion ratios (e.g. to remove high mass column bleed ions) can only be done by manually editing the JCAMP file. However, this must be done with caution, or the entire library can be corrupted!

Other Systems

Hewlett Packard libraries are not readily converted to other manufacturer's formats without the use of commercial or other software. One very powerful software package is called Mass TransitTM, published by Palisade Corporation. This program has the ability to accurately inter-convert a very wide range of mass spectral libraries, including most formats for Finnigan, Varian, Perkin Elmer and Shimadzu. Check out the links above for a fuller description of their software and pricing.

The committee is grateful to Palisade Corporation for providing us with a complimentary copy of their software to assist with making our library available in different manufacturer's formats.

*Now Agilent

Return to main page