The COMSPARI Homepage

In our GC/MS laboratory, we have often questions of the kind "how to differentiate these two samples", and the program is a real helper for this :-) ... pleased to see that you put it under GPL. Thank you very much for that! If you want, we can test future versions here (we use Chemstation and XCalibur).

... another analysis, which finally turned out to be a contamination (Dichlormethane) coeluting under a solvent peak. The CH2Cl2 signal was superimposed by the solvent peak - I suppose, without Comspari I would never have found the contamination."

What is COMSPARI?

COMSPARI is the acronym for COMparison of SPectral And Retention Information. It is a software that has been written to facilitate the analysis of "paired" samples, i.e. samples that are almost identical yet present some qualitative difference. The software was originally written for the analysis of data files produced by GC/MS and LC/MS, but can be used for other techniques, too.

COMSPARI was first described in a publication by J. E. Katz, J. Hau, D. S. Dumlao, and S. Clarke: "A New Technique (COMSPARI) to Facilitate the Identification of Minor Compounds in Complex Mixtures by GC/MS and LC/MS: Tools for the Visualisation of Matched Datasets". J. Amer. Soc. Mass Spectrom. 15 (2004), 580-584.

cdf2ascii, included with the COMSPARI package, is a small utility program that allows to convert mass spectrometric data files from the netCDF (aka "ANDI-MS") format into plain ASCII format. It is probably also of use for anybody who desires to write programs or use existing software that want to deal with flat ASCII files rather than NetCDF files.

Since fall 2003, the software is in a fully operational stage. It has a command-line interface and a simple (yet very effective!) graphic display based on gnuplot. The program is principally developed under Linux and should generally compile on any POSIX-compliant platform; in addition, it is also operational under recent versions of Microsoft Windows. We provide both the source code and the binaries in the download section below.

There are some informational files that are included with the distribution snapshots that we are linking to here for quick reference; these are: README and LICENSE.

Screenshots

Authors

The authors are Jonathan Katz (original author) and Jörg Hau.

License

COMSPARI and its related packages are Free Software and are published under the GNU General Public License (GPL). You can redistribute it and/or modify it under the terms of the GPL, 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

The comspari software package depends on several other software packages.

Note for Microsoft Windows users: We have had reports that the files sometimes "do not open" under MS Windows XP. The reason is apparently that Windows XP breaks the filenames if you try to open a file on-the-fly. Workaround: Right-click on the link > "Save Target as ..." > make sure that the file extension - tgz - is preserved! You can then open the downloaded file normally.

User

For "normal" use, you just need:

the "core files" (Size: 144k , comspari-20041118-prebuilt.tgz ). This archive contains comspari and cdf2ascii (pre-compiled for Linux and Win32) and their source code. It does not include any sample files. If you already have COMSPARI working, this is probably what you are looking for to stay updated - it is very unlikely that we will be changing the other packages in the near future.
gnuplot, a scientific data plotting package,
and some data files in netCDF format - optionally you can download our sample data files (Size: 3.2M , comspari-20030822-sample.tgz ): This archive file contains the two datasets were used to produce the paper mentioned above. The files are "ko" (knock-out) and "wt" (wild type), in netCDF format. Using these files, you can try out the COMSPARI package without generating your own dataset(s).

Intrepid User

If you are an intrepid user that is not afraid of working with BETA versions, you have come to the right place:

Download the latest Beta: comspari-current-BETAprebuilt.tgz (Size: 2.7M , comspari-20041103-BETAprebuilt.tgz ). You have been warned: This is beta ... yet it implements some new features, such as mass "binning" and the possibility to deal with MS/MS data.
gnuplot, a scientific data plotting package,
and some data files in netCDF format - optionally you can download our sample data files (Size: 3.2M , comspari-20030822-sample.tgz ).

Developer

If you want to modfify and/or recompile comspari or cdf2ascii, you need the files above (i.e., "core" and gnuplot), and a C compiler.
If you want to modify and/or recompile cdf2ascii, you will also need the netCDF library (from ftp.unidata.ucar.edu/pub/netcdf) and in particular the ANDI-MS library (http://sourceforge.net/projects/andi/) to work with netCDF data.
In addition, it is useful to link comspari to the GNU readline library (at ftp.gnu.org/pub/gnu/readline).

To Do

The comspari software is in a fully operational stage. However, the more you use it, the more options come to mind ;-) ... a few of those possibilities are:

possibility to specify "non-neigbouring" masses for chromatogram display (partially implemented via the reading of external mass lists)
write documentation ;-)

Things that should be fixed in the future:

disable offset (or provide different offset) in mass chromatogram mode (yet ... there is use for a deliberate mass offset when looking for modified substrates)
more error checking, e.g. on output filename and on input ranges
fix the auto-prefix calculation (cdf2ascii)
clean up and "modularize" code

History

2006-05: Since fall 2004, there has been no "active" development ... simply because the software is stable and performs exactly to our needs ;-) As we have not received any bug reports either (and both authors have somewhat changed their field of work), no further work is planned "for the time being".
2004-11-18: cdf2ascii now supports conversion of multiple files, i.e. you can use wildcards ("my*.cdf") on the command line.
2004-11-16: Major "relooking" of the download section of this website.
2004-11-15: Some convenient additions to v20041115. cdf2ascii and comspari have now flags for easy compilation under Win32, and comspari has the possibility to specify the path/to/gnuplot on the command line.
2004-11-10/12: A poster (pdf, 900 kB) discussing the latest version of comspari was presented at the 21st "Montreux" LC/MS conference.
2004-11-02: A long pause, but filled with activity ... comspari has now the capability to load lists of "preselected" m/z traces. This allows e.g. direct interfacing to the CODA Component Detection Algorithm, as it is (for example) implemented in MSGraph. - This feature supports currently lists with (a) only m/z information (one per line), (b) m/z and MCQ values, and even (c) m/z and two MCQ values from merged m/z lists. Yes, you can now use MCQ thresholds to exclude "uninteresting" traces ;-)
2004-03-23: The first paper about comspari is published: J. E. Katz, J. Hau, D. S. Dumlao, and S. Clarke. "A New Technique (COMSPARI) to Facilitate the Identification of Minor Compounds in Complex Mixtures by GC/MS and LC/MS: Tools for the Visualisation of Matched Datasets". J. Amer Soc. Mass Spectrom. 15 (2004), 580-584.
2004-03-09: Finally an update to the beta version of comspari. This should handle LCQ files pretty well and do mass binning at masses other than 1. Modified output to include multiple decimal places; rounding was causing problems with duplicate m/z entries in some non-compspari applications...
2003-01-15: comspari: added difference plot to subtract datasets on-the-fly.
2003-10-12: comspari: minor step bug fix, "?" now invokes help
2003-10-03: cdf2ascii: fixed a memory allocation bug (not allocating enough memory at times); comspari: scaling now works with floats (20030926)
2003-09-23: cdf2ascii: added -i (info), obsoleting "cdfinfo". - "-o" now specifies an output dir, "-O" specifies a dir and prefix for output files. - output file suffices now are .chro (was .mz) and .spec (was .scan).; comspari: now has nice command-line and mouse annotation features :-); website: Added "readline" to the required packages distribution.
2003-09-04: Minor changes in comspari-20030904-prebuilt.tgz; comspari: Removed 'GetKey()'/'Input()' and reverted to a line processing system for command processing; this fixed all white space and buffer issues known.; cdf2ascii: Made the prefix option fully descriptive, i.e., if a prefix is specified the source filename does not contribute to the definition of the output prefix.; website: Made Jörg Hau's better looking version of the website the live version.
2003-08-29: comspari: Fixed bug in GetKey() that caused double display of TIC traces. - Corrected line colors for TIC. - Printing routine works now as it was always intended :-).; cdf2ascii: Introduced a control structure (to hold all those flags together ;-). - Added minscan/maxscan parameter. - All min/max parameters (scan and m/z) are now also valid for raw dump. - Replaced *tic by calculation on-the-fly. - Replaced code for raw scan dump by the same routine from 'cdfread.c'. - Fixed bug in the scan counter in open_cdf_ms(). - Fixed potential bug in min/max scan/mass range assignment. - ASCII files now with header line. - Added various error checks.
2003-08-22: Split packages so that you can just download new versions without having to re-download the other stuff.
2003-08-21: Bugfix release comspari-20030822-prebuilt.tgz.; cdf2ascii: Fixed an error in TIC file output.
2003-08-19: New functionalities in comspari-20030819.tgz; cdf2ascii: Now outputs a PREFIX.tic file.; comspari: Now has functionality to show TIC files, either overlapped and offset or head-to-tail.
2003-08-18: Code optimisation. comspari-20030818.tgz.; cdf2ascii: Put back in the -m/M and -R (formerly -S) functionality. - -o prefix specifies the entire prefix (i.e., do: -o out/wt). - Changed some code formatting and memory allocation code.
2003-08-14: Major changes in comspari-20030814.tgz.; cdf2ascii: More resistant to misuse/errors :-) . - Output filename is now automagically derived from input filename. - Ported integer-mass processing (also for profile data) from "cdf2msg.c". - Can apply a mass defect (default is 0.3 at m/z 1000). - Changed ASCII filename convention, now "file_0123.[mz|scan]". - Changed some variable names ("scan" and "mass" instead of x, y ;-). - Introduced a control structure that holds min/max info for mass and scan; this can e.g. be used to convert only a part of the file. - Removed "raw scan" and "m/z range" functionality -m/M, -S.; comspari: Added command line parser. - Data files now listed on command line. - Mass Spectra now plotted as histograms.
2003-08-11: cdf2ascii: Added m/z range functionality (-m -M) and "raw scan dump" functionality (-S).
2003-08-07: comspari-20030807.tgz, first internal release.