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In vitro and in silico processes to identify differentially expressed proteins.
- Source :
-
Proteomics [Proteomics] 2004 Aug; Vol. 4 (8), pp. 2333-51. - Publication Year :
- 2004
-
Abstract
- We present an integrated proteomics platform designed for performing differential analyses. Since reproducible results are essential for comparative studies, we explain how we improved reproducibility at every step of our laboratory processes, e.g. by taking advantage of the powerful laboratory information management system we developed. The differential capacity of our platform is validated by detecting known markers in a real sample and by a spiking experiment. We introduce an innovative two-dimensional (2-D) plot for displaying identification results combined with chromatographic data. This 2-D plot is very convenient for detecting differential proteins. We also adapt standard multivariate statistical techniques to show that peptide identification scores can be used for reliable and sensitive differential studies. The interest of the protein separation approach we generally apply is justified by numerous statistics, complemented by a comparison with a simple shotgun analysis performed on a small volume sample. By introducing an automatic integration step after mass spectrometry data identification, we are able to search numerous databases systematically, including the human genome and expressed sequence tags. Finally, we explain how rigorous data processing can be combined with the work of human experts to set high quality standards, and hence obtain reliable (false positive < 0.35%) and nonredundant protein identifications.
- Subjects :
- Chromatography instrumentation
Chromatography methods
Computational Biology
Databases, Factual
Humans
Information Management instrumentation
Mass Spectrometry instrumentation
Mass Spectrometry methods
Peptides analysis
Proteins genetics
Proteins metabolism
Reproducibility of Results
User-Computer Interface
Body Fluids chemistry
Gene Expression Profiling
Information Management methods
Proteins analysis
Proteins chemistry
Proteomics methods
Subjects
Details
- Language :
- English
- ISSN :
- 1615-9853
- Volume :
- 4
- Issue :
- 8
- Database :
- MEDLINE
- Journal :
- Proteomics
- Publication Type :
- Academic Journal
- Accession number :
- 15274127
- Full Text :
- https://doi.org/10.1002/pmic.200300840