Analytical and Bioanalytical Chemistry

, Volume 390, Issue 5, pp 1327–1342 | Cite as

Application of partial least squares discriminant analysis and variable selection procedures: a 2D-PAGE proteomic study

  • Emilio Marengo
  • Elisa Robotti
  • Marco Bobba
  • Alberto Milli
  • Natascia Campostrini
  • Sabina Carla Righetti
  • Daniela Cecconi
  • Pier Giorgio Righetti
Paper in Forefront

Abstract

2D gel electrophoresis is a tool for measuring protein regulation, involving image analysis by dedicated software (PDQuest, Melanie, etc.). Here, partial least squares discriminant analysis was applied to improve the results obtained by classic image analysis and to identify the significant spots responsible for the differences between two datasets. A human colon cancer HCT116 cell line was analyzed, treated and not treated with a new histone deacetylase inhibitor, RC307. The proteins regulated by RC307 were detected by analyzing the total lysates and nuclear proteome profiles. Some of the regulated spots were identified by tandem mass spectrometry. The preliminary data are encouraging and the protein modulation reported is consistent with the antitumoral effect of RC307 on the HCT116 cell line. Partial least squares discriminant analysis coupled with backward elimination variable selection allowed the identification of a larger number of spots than classic PDQuest analysis. Moreover, it allows the achievement of the best performances of the model in terms of prediction and provides therefore more robust and reliable results. From this point of view, the multivariate procedure applied can be considered a good alternative to standard differential analysis, also taking into account the interdependencies existing among the variables.

Keywords

Two-dimensional maps Proteomics Multivariate statistical methods Partial least squares discriminant analysis Variable selection procedures 

Abbreviations

BE

backward elimination

CHAPS

3-[(3-cholamidopropyl)dimethylammonium-1-propanesulfonate

DA

discriminant analysis

HDAC

histone deacetylase

HSPA5

heat shock 70-kDa protein 5

IEF

isoelectric focusing

IPG

immobilized pH gradient

LDA

linear discriminant anlysis

LV

latent variable

MALDI-TOF-TOF

matrix-assisted laser desorption/ionization tandem time-of-flight

PAGE

polyacrylamide gel electrophoresis

PCA

principal component analysis

PLS

partial least squares

PRDX1

peroxiredoxin I

RMSE

root mean square error

RMSEC

root mean square error in calibration

RMSECV

root mean square error in cross-validation

RMSEP

root mean square error in prediction

RP-HPLC-ESI MS/MS

reversed-phase high-performance liquid chromatography electrospray ionization tandem mass spectrometry

SDS

sodium dodecyl sulfate

SIMCA

soft-independent model of class analogy

SSP

standard spot

STMN1

stathmin 1

Tris

tris(hydroxymethyl)aminomethane

Notes

Acknowledgements

The authors thank A. Vindigni and L. Zolla for mass spectrometry experiments. This work was supported in part by a grant from Fondazione Cariplo to P.G.R.

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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Emilio Marengo
    • 1
  • Elisa Robotti
    • 1
  • Marco Bobba
    • 1
  • Alberto Milli
    • 2
  • Natascia Campostrini
    • 3
  • Sabina Carla Righetti
    • 4
  • Daniela Cecconi
    • 2
  • Pier Giorgio Righetti
    • 5
  1. 1.Dipartimento di Scienze dell’Ambiente e della VitaUniversità degli Studi del Piemonte OrientaleAlessandriaItaly
  2. 2.Dipartimento Scientifico e Tecnologico, Laboratorio di ProteomicaUniversità degli Studi di VeronaVeronaItaly
  3. 3.Dipartimento di Medicina Clinica e Sperimentale, Sezione di Medicina Interna BUniversità degli Studi di VeronaVeronaItaly
  4. 4.Istituto Nazionale per lo Studio e la Cura dei TumoriMilanoItaly
  5. 5.Dipartimento di ChimicaMateriali e Ingegneria Chimica “Giulio Natta”MilanoItaly

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