On the preprocessing of mass spectrometry proteomics data

M. Cannataro, P. H. Guzzi, T. Mazza, G. Tradigo, P. Veltri

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Citations (Scopus)

Abstract

Mass-Spectrometry (MS) based biological analysis is a powerful approach for discovering novel biomarkers or identifying patterns and associations in biological samples. Each value of a spectrum is composed of two measurements, m/Z (mass to charge ratio) and intensity. Even if data produced by mass spectrometers contains potentially huge amount of information, data are often affected by errors and noise due to sample preparation and instrument approximation. Preprocessing consists of (possibly) eliminating noise from spectra and identifying significant values (peaks). Preprocessing techniques need to be applied before performing analysis: cleaned spectra may then be analyzed by using data mining techniques or can be compared with known spectra in databases. This paper surveys different techniques for spectra preprocessing, working either on a single spectrum, or on an entire data set. We analyze preprocessing techniques aiming to correct intensity and m/Z values in order to: (i) reduce noise, (ii) reduce amount of data, and (iii) make spectra comparable.

Original languageEnglish
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages127-131
Number of pages5
Volume3931 LNCS
DOIs
Publication statusPublished - 2006
Event16th Italian Workshop on Neural Nets, WIRN 2005, and International Workshop on Natural and Artificial Immune Systems, NAIS 2005 - Vietri sul Mare, Italy
Duration: Jun 8 2005Jun 11 2005

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3931 LNCS
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other16th Italian Workshop on Neural Nets, WIRN 2005, and International Workshop on Natural and Artificial Immune Systems, NAIS 2005
CountryItaly
CityVietri sul Mare
Period6/8/056/11/05

Fingerprint

Proteomics
Mass Spectrometry
Biomarkers
Mass spectrometers
Spectrum analysis
Mass spectrometry
Data mining
Preprocessing
Noise
Data Mining
Spectrum Analysis
Databases
Spectrometer
Preparation
Charge
Entire
Approximation

Keywords

  • Data cleaning
  • Data preprocessing
  • Mass Spectrometry

ASJC Scopus subject areas

  • Computer Science(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Theoretical Computer Science

Cite this

Cannataro, M., Guzzi, P. H., Mazza, T., Tradigo, G., & Veltri, P. (2006). On the preprocessing of mass spectrometry proteomics data. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 3931 LNCS, pp. 127-131). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3931 LNCS). https://doi.org/10.1007/11731177_19

On the preprocessing of mass spectrometry proteomics data. / Cannataro, M.; Guzzi, P. H.; Mazza, T.; Tradigo, G.; Veltri, P.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 3931 LNCS 2006. p. 127-131 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3931 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Cannataro, M, Guzzi, PH, Mazza, T, Tradigo, G & Veltri, P 2006, On the preprocessing of mass spectrometry proteomics data. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). vol. 3931 LNCS, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 3931 LNCS, pp. 127-131, 16th Italian Workshop on Neural Nets, WIRN 2005, and International Workshop on Natural and Artificial Immune Systems, NAIS 2005, Vietri sul Mare, Italy, 6/8/05. https://doi.org/10.1007/11731177_19
Cannataro M, Guzzi PH, Mazza T, Tradigo G, Veltri P. On the preprocessing of mass spectrometry proteomics data. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 3931 LNCS. 2006. p. 127-131. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/11731177_19
Cannataro, M. ; Guzzi, P. H. ; Mazza, T. ; Tradigo, G. ; Veltri, P. / On the preprocessing of mass spectrometry proteomics data. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 3931 LNCS 2006. pp. 127-131 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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