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Multivariate analyses for biomarkers hunting and validation through on-tissue bottom-up or in-source decay in MALDI-MSI: application to prostate cancer.
- Source :
-
Analytical and bioanalytical chemistry [Anal Bioanal Chem] 2011 Jul; Vol. 401 (1), pp. 149-65. Date of Electronic Publication: 2011 Apr 26. - Publication Year :
- 2011
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Abstract
- The large amount of data generated using matrix-assisted laser desorption/ionization mass spectrometric imaging (MALDI-MSI) poses a challenge for data analysis. In fact, generally about 1.10(8)-1.10(9) values (m/z, I) are stored after a single MALDI-MSI experiment. This imposes processing techniques using dedicated informatics tools to be used since manual data interpretation is excluded. This work proposes and summarizes an approach that utilizes a multivariable analysis of MSI data. The multivariate analysis, such as principal component analysis-symbolic discriminant analysis, can remove and highlight specific m/z from the spectra in a specific region of interest. This approach facilitates data processing and provides better reproducibility, and thus, broadband acquisition for MALDI-MSI should be considered an effective tool to highlight biomarkers of interest. Additionally, we demonstrate the importance of the hierarchical classification of biomarkers by analyzing studies of clusters obtained either from digested or undigested tissues and using bottom-up and in-source decay strategies for in-tissue protein identification. This provides the possibility for the rapid identification of specific markers from different histological samples and their direct localization in tissues. We present an example from a prostate cancer study using formalin-fixed paraffin-embedded tissue.
- Subjects :
- Amino Acid Sequence
Animals
Formaldehyde
Humans
Male
Molecular Sequence Data
Multivariate Analysis
Paraffin Embedding
Prostate pathology
Prostatic Neoplasms pathology
Rats
Rats, Wistar
Biomarkers, Tumor analysis
Prostatic Neoplasms diagnosis
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization methods
Subjects
Details
- Language :
- English
- ISSN :
- 1618-2650
- Volume :
- 401
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- Analytical and bioanalytical chemistry
- Publication Type :
- Academic Journal
- Accession number :
- 21519967
- Full Text :
- https://doi.org/10.1007/s00216-011-5020-5