Nicola Barbarini

Paolo Magni

Riccardo Bellazzi

BMC Bioinformatics

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BioMed Central
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BMC Bioinformatics
Open AccessPoster presentation
A procedure to decompose high resolution mass spectra
Nicola Barbarini*, Paolo Magni and Riccardo Bellazzi
Address: Department of Computer Science and Systems, University of Pavia, Italy
Email: Nicola Barbarini* - nicola.barbarini@unipv.it
* Corresponding author    
Background
The proposed procedure can be applied to two different
studies. The first one is discovering proteomic patterns by
SELDI-TOF mass spectra. The application of the procedure
has the aim of finding how many proteins are represented
in the spectrum of the sample, among which to search the
biomarker.
The second study is the protocol composed by 2D-GE sep-
aration, MS MALDI-TOF and PMF (Peptide Mass Finger-
printing) algorithm, used to identify proteins in a sample.
The aim of the application of the proposed procedure to
PMF data is the automatic choice of the masses to use as
input for PMF algorithm.
Methods
The algorithm analyses a set of N mass spectra already pre-
processed by a quite standard procedure (baseline sub-
traction, smoothing filtering and normalization). Then it
looks for all the isotopic peaks contained in the median
spectrum by computing the position of all the local
maxima. Next it extracts all the isotopic distributions
which are in the median spectrum, analyzing every iso-
topic peak from the one with highest intensity using a
model based on chemical knowledge and statistical prop-
erties (the coefficient of correlation).
At last the isotopic distributions with the coefficient of
correlation among spectra above a threshold are grouped
together.
Results
First, the procedure was applied to a dataset of SELDI-TOF
mass spectra from the human serum of 216 different sub-
jects. With this algorithm we found 7216 isotopic peaks
and then 118 isotopic distribution which we assembled in
10 groups with a coefficient of correlation threshold of
0,72. Every group seems to be associated with a single pro-
tein.
Then, we analyzed with the same procedure a MALDI-TOF
spectrum of PDIA1_MOUSE enzymatically digested com-
posed of 162 scans. We found 4700 isotopic peaks and
then we assembled the first 60 isotopic distributions in 4
groups with a coefficient of correlation threshold of 0,75.
The group not produced by the matrix contains the masses
of the peptides.
Conclusion
The correlation coefficient among spectra of different sub-
jects/scans is a mean never utilized by the current algo-
rithms for the extraction of isotopic distributions. This
solution reduces the speed of the algorithm but it seems
to manage very well the situations of overlapping situa-
tions and the hard cases.
The most innovative part is the phase of isotopic distribu-
tion grouping by correlation coefficient. The application
of this procedure shows some good results both for group-
ing isotopic distributions of the same proteins and for
finding the masses of the enzymatically digested peptides
in PMF experiment.
from Third International Society for Computational Biology (ISCB) Student Council Symposium at the Fifteenth Annual International Conference on Intel-
ligent Systems for Molecular Biology (ISMB)
Vienna, Austria. 21 July 2007
Published: 20 November 2007
BMC Bioinformatics 2007, 8(Suppl 8):P6 doi:10.1186/1471-2105-8-S8-P6
<supplement> <title> <p>Highlights from the Third International Society for Computational Biology (ISCB) Student Council Symposium at the Fifteenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB)</p> </title> <editor>Nils Gehlenborg, Manuel Corpas and Sarath Chandra Janga</editor> <sponsor> <note>The organizing committee would like to thank the International Biowiki Contest funded by the Korean Bioinformation Center (KOBIC) and the Institute for Systems Biology for financial contributions that made the publication of these highlights possible.</note> </sponsor> <note>M eting abstracts – A singl PDF co tai ing all abstracts in this Supplement is available <a href="http://www.biomedcentral.com/content/pdf/1471-2105-8-S8-full.pdf">h re</a></note> <url>http://www.biomedcentral.com/content/pdf/1471-2105-8-S8-info.pdf</url> </supplement>
This abstract is available from: http://www.biomedcentral.com/1471-2105/8/S8/P6
© 2007 Barbarini et al; licensee BioMed Central Ltd. 


A procedure to decompose high resolution mass spectra

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A procedure to decompose high resolution mass spectra

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