The cdfread homepage

Overview

cdfread is a program that implements the routines to read mass spectra and mass chromatograms from data files in netCDF ("Andi-MS") format.

The program has a command-line interface and a simple graphic display based on gnuplot. It supports mouse zoom and manual peak annotation.

The main purpose of the program is to provide platform-independent routines to access netCDF files, e.g. to select any given spectrum or any mass chromatogram. Centroid and profile data are supported. - Please note that this is NOT a full-fledged data evaluation suite ... albeit it is now in a state where you could write something like that around it without too much effort ;-).

At a glance

• Reads CDF data files from (almost) any MS manufacturer on (almost) any computer platform.
• Call most functions directly, with a single command.
• Zoom by a point-and-draw action of the mouse.
• Visualize mass spectra and mass chromatograms.
• Visualize mass chromatograms of a mass range.
• Get graphics in high-quality Postscript format.
• Runs under Linux and MS-Windows (and should generally compile on any POSIX-compliant platform).
• Freely available under the terms and conditions of the GNU Public License (GPL)

Getting CDF files

To get CDF files from your data acquisition package:

• Micromass MassLynx: Start > Programs > MassLynx > DataBridge.
• Finnigan Xcalibur: "Roadmap View" > Tools > File Converter.
• Finnigan ICIS2: ICIS Executive > File > Convert > "DAT to ANDI-MS".
• Agilent ChemStation: File > "Export MS Data to AIA"; there is also a batch mode from the same menu.
• Sciex Analyst: Reportedly there is a macro available upon request from Sciex.
• (others? Please contribute if you can ...)

System Requirements

The software runs at least under Linux and the 32-bit flavours of MS-Windows.

The graphic display makes use of gnuplot, a free software for scientific data plotting. You need version 4 or later.

To re-compile cdfread from scratch, a standard-compatible C compiler is required, and a few libraries - notably the netCDF library, and the public part of the original ANDI-MS (netCDF) distribution. Detailed instructions are provided in the documentation.

Status: Production!

The software is in use since 2001. It has been updated a few times, but no major changes were introduced. I have good reasons to believe that it is in a stable state.

License

This software is Free Software and are published under Version 2 of the GNU General Public License (GPL). You can redistribute it and/or modify it under the same terms, which ensures that its source code is free and that any derivatization, or implementation of it in other software, will also remain free.

The difference between "free software" and "freeware" is of legal importance. If you do not understand any portion of this license, please seek appropriate professional legal advice. If you do not or if - for any reason - you can not accept all of the conditions of the GPL, then you must not use nor distribute this software.

Download

Since early 2009, this project is hosted at sourceforge.net. To download, you have several possibilities:

• Visit the Sourceforge project page.
• If you have a subversion client installed, run svn checkout https://svn.code.sf.net/p/cdfread/code/ cdfread

The author is Jörg Hau.

I gratefully acknowledge a number of people that have, direct or indirect, contributed to this software:

• David Stranz (for pointing me to the initial ANDI-MS distribution and code)
• Herbert Kratky (for useful hints on compiling)
• Arlindo da Silva (for making his pre-compiled libraries publicly available)
• Unidata (for making all the nice netCDF stuff available)
• Jonathan Katz (for great inspiriation around the menu)
• Ethan Merritt (for valuable gnuplot hints)
• Steve Cepa (for various manufacturer's CDF conversions)

A derivative of cdfread is cdf2ascii, which is part of the COMSPARI software. It allows to convert netCDF files into plain ASCII files, with lots of processing options.