Jörgs Mass Spectrometry and Bioinformatics Page

HitKeeper

HitKeeper is a database application for use in BioInformatics. It is intended to help bioinformatic researchers with "friendly" tools. Originally designed for the investigation of the relationships between protein sequences and motifs defined (or predicted) on them, it effectively handles the redundancy of biological databases, incremental updates, supports taxonomy and has a sophisticated query engine.

HitKeeper was - and is - developed and is maintained by Marco Pagni, with contributions from myself and many others ;-). It is mainly written in Perl/SQL and published under the GNU Public License (GPL). It was first described in J. Hau, M. Muller, M. Pagni, "HitKeeper, a generic software package for hit list management", Source Code for Biology and Medicine 2 (2007), 2.

HitKeeper has its own homepage at http://hitkeeper.sourceforge.net/.

COMSPARI

COMSPARI is the acronym for COMparison of SPectral And Retention Information. It is a software to facilitate the analysis of "paired" samples, i.e. samples that are almost identical yet present some qualitative difference, by GC/MS and LC/MS as well as other techniques. COMSPARI should thus be particularly useful for applications in metabolomics and proteomics.

COMSPARI was developed and is maintained by Jonathan Katz (with some contributions from myself ;-) and was first described in 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 Visualization of Matched Datasets", J. Amer. Soc. Mass Spectrom. 15 (2004), 580-584.

A "by-product" of this development work is cdf2ascii, which is based on cdfread. It allows to convert netCDF files into plain ASCII files, with lots of processing options and is part of the COMSPARI package.

• COMSPARI has its own homepage at http://www.biomechanic.org/comspari/.
• Its development has been a topic of the "Brave GNU World" column in 2005; for an example copy, see e.g. linuxpromagazine.com (pdf - as of 2018, link seems to be dead?).

CDF reader

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 provides a command-line interface and a simple graphic display based on gnuplot. It supports mouse zoom and manual peak annotation. Centroid and profile data are supported.

CDFread has its own homepage at http://cdfread.sourceforge.net/.

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

LC/MS Data Evaluation

MSGraph is a program designed for the interactive, fast, qualitative analysis of mass spectrometric (MS) data. It is a tool to provide fast and simple access to all the information contained in an LC/MS analysis run. Key features:

• Call most functions directly, with a single keystroke or mouse click.
• Use the "eagle's view" (2D) display to visualise of all the information of an analysis run: time, scan number, m/z and signal intensity at the same time.
• Use CODA COmponent Detection Algorithm to detect compounds and to perform "intelligent" background subtraction.
• Zoom by a point-and-draw action of the mouse.
• Switch between all displays with just one mouse click or keystroke.
• Browse spectra and mass chromatograms with one keystroke or mouse click.
• Integrate mass chromatograms manually using the mouse.
• Keep track of "interesting" mass traces by writing them to file.
• Get graphical data in high-quality Postscript format, including color output.
• Export data - mass spectra, mass chromatogram, integration results and even 2D - as ASCII files, e.g. for use with other graphics or spreadsheet software.
• ... and it is Free Software, published under version 2 of the GNU Public License (GPL)!

Several related tools are available, including programs to read data files in netCDF and mzXML format.

MSGraph has its own homepage at http://msgraph.sourceforge.net/.

The Analyses Database

The Analyses Database is a collection of software to archive and to track files. It was written with the backup and archival of data from analytical instruments in mind and was first described in a paper by J. Hau and L. Fay, "Practical Approach to Archival and Retrieval of Analytical Data in the Laboratory", published in Analyst 126 (2001), 1194-1199.

This software has been used in my (former) laboratory for almost a decade now and has performed flawlessly - thus I have good reasons to say that it performs as designed and that it is in a stable state.

The project has its own homepage at http://labdb.sourceforge.net/.

The Chemicals Database

The Chemicals Database is a simple yet effective approach to track a stock of products. It provides "product catalogue" that is accessible from any workplace over http. — Although the documentation describes the handling of a stock of chemicals in a laboratory in particular, the system can easily be adapted to any other "items" such as samples, spare parts, tools and other inventory.

The application was developed based on The Analyses Database and implemented at remarkably low cost (e.g. no license fees at all) in short time, using the Linux operating system and standard off-the-shelf computer equipment. The system went from test phase to production in less than one week. In my (former) laboratory it helped us to improve efficiency and to save cost, e.g. by avoiding multiple orders of identical products.

The project has its own homepage at http://chemicaldb.sourceforge.net/.

Isotope Pattern

isotope is a command-line utility to calculate the isotope pattern for a given chemical formula. It allows to run calculations interactively, in batch mode, via the command line, or (using a webserver) via a web interface. You can easily integrate it into your laboratory workflow, even using fully automated data processing.

Isotope has its own homepage at http://isopat.sourceforge.net/.

HiRes MS

hr (or HiRes, for "High Resolution") is a simple program to perform a common task in mass spectrometry: calculate the possible elemental compositions that fit a given mass. It allows to run calculations in batch mode, via the command line, or (using a webserver) via a web interface. You can easily integrate it into your laboratory workflow, even using fully automated data processing.

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Isotope has its own homepage at http://hires.sourceforge.net/.

Peak Matching

match is a program to perform the calculations required during manual peak matching on a sector field mass spectrometer. Although this task is performed automatically on modern instruments, there are still some colleagues out there that [have to] do peak matching manually. The original program was written sitting at the console of a VG7070 back in 1994, but of course it is applicable to any sector field MS that is equipped with a unit for manual peak matching.

The program runs under MS-DOS, or in a "DOS window" under various flavours of MS-Windows. It is copyrighted by me, but use is free - see the file README.TXT included in the archive.

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Click here to download the program. This includes a few reference data files. The latest version is 1.2.

Linux to access
other workstations

Do you run one or more machines under Unix or VMS and do you wish you had a cheap second (or third or fourth ...) access to it, with full graphical capabilities? Well, this little article is for you.

How to use Linux to share your High-end Workstation.

NMR spectrum viewer

This has nothing to do with mass spectrometry, but anyway ;-)

bruread-nmr is a simple a program to access and display NMR data in the Bruker XWIN-NMR format. You can display either the real or the imaginary part of the spectrum, or the FID. - The program has a command-line interface and a graphic display based on gnuplot. It supports mouse zoom and manual peak annotation. However, please note that this is merely an NMR spectrum viewer - it is not a data evaluation suite.

The project has its own homepage at http://bruread.sourceforge.net/.

Gnuplot

Map view in gnuplot

set pm3d map
set yrange [*:*] reverse
splot 'sample.dat' matrix

A nice 2D-Plot color palette is: black - brown - dark red - red ... white on "sky-blue" background (seen on SGMS 2003).

Plotting mass spectra in gnuplot

set xlabel "m/z"
set ylabel "Abundance"
set tics out
set xtics nomirror
set border 31
set nokey

Plotting UV spectra in gnuplot

set nogrid
set nokey
set nolabel
set size ratio 1 1,1
set tics in
set xlabel "nm"
set ylabel "mAU"
set xrange [180:400]
set data style lines
#set term postscript eps solid "Times-Roman"
set term aifm
set title "Name of this compound"
set outp "data.ai"
plot "data.dat"

Re-scaling gnuplot eps files to print in full-size A4

sed '/%%EndComments/ a\
90 rotate\
-60 -670 translate\
2.1 2.1 scale' file.eps | lpr -P NameOfPrinterQueue

We can use filledcurve to print chromatograms

plot sin(x) with filledcurve y1=-0.5
plot sin(x) with filledcurve x1

Plotting of multiple data files by wildcard

list = system('ls *red[0-9].dat *green*dat | sort -t. -k2')  # get a sorted list via system call
t(s) = (s2 = s[15:*], s2[0:strlen(s2)-4])                    # remove first 15 and last 4 chars from filenames
set ylabel "Volt"
set xlabel "hours"
plot for [file in list] file using ($1/3600):2 w lin title t(file)

Data processing

Derivative with awk:

#! /usr/bin/awk -f
BEGIN { firstline = 1 }

#$0 !~ ^# { if (firstline == 1) {
{ if (firstline == 1) {
    old_x = 1
    old_y = 1
    firstline = 0
  } else {
    print (old_x + $2)/2.0, "\t", (old_y - $3)/(old_x - $2), "\t"
    old_x = $2
    old_y = $3
  }
}

Numerical differentiation with octave:

load 'data.dat'
x=data(:,1);
y=data(:,2);
dx=diff(x);
dy=diff(y);
# now we need to get them to same array length. interpolate:
points = [x(1:numel(x)-1)+dx(1)/2, diff(data(:,2))./dx];
fd=fopen("outfile","wt")
fprintf(fd, "%14.6f %14.6f\n", reshape(points', 1, numel(points)));
fclose(fd);
disp("Done!");

Low-pass filter 1st order with gnuplot and awk. d is the damping:

gnuplot> plot "< awk 'print $2" < file.dat" using 1 with lp
gnuplot> plot "< awk -v d=2 'i=(d*i+$2)/1+d); print i' < file.dat" using 1 with lp

Data Visualisation

• Gnuplot, a powerful command-line plotting utility. Available for many platforms, including Linux, DOS and Windows. A quick but thorough tutorial is at HP Gavin's page. More information is available in the FAQ. - Ethan Merritt is an active gnuplot developer and has a page with actual patches and on-going work and N. Devillard has written a number of gnuplot interfaces in ANSI C and the blog of Gnuplotter provides lots of tricks and nice visual stuff.
• Gri is "an extensible plotting language for producing scientific graphs, such as x-y plots, contour plots and image plots". There is (imho ;-) some similarity to gnuplot.
• If the capabilities of gnuplot are not enough for you, try Grace.

Mass Spectrometry

• Archives for sci.techniques.mass-spec.
• SGMS, the Swiss Group for Mass Spectrometry.
• Atomic weights and isotopic compositions at NIST.
• ms-utils.org, a repository for and a collection of links to free software and code snippets for the visualization and analysis of mass spectrometry data.
• mMass, an open-source mass spectrometry tool.
• The 1994 example code to read netCDF MS datafiles ("andi-MS") is now available at sourceforge.net. More general information about the netCDF standard is available at Unidata and for download via ftp. A number of pre-built libraries for different OS are located in the /pub/netcdf/contrib tree.

Bioinformatics

• The Swiss Institute of Bioinformatics, home of the myHits website ... which is powered by Hitkeeper ;-)
• Source Code for Biology and Medicine, an Open Access journal.

Neuroscience

In the frame of a few projects have been working on neurosignal data processing. Here are some links that I found useful:

• BioSig, an open source software library for biomedical signal processing, including EEG, ECoG, ECG, EOG, EMG, etc.
• EEGLAB, "an interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data".
• A description of the BioSemi file format.
• The European Data Format (EDF), a file format for exchange and storage of multichannel biological and physical signals.

Some Databases, Literature etc.

• FreePatentsOnline.com. Limited to US patents.
• The German Patent- und Markenamt.
• Query the PubMed database.