Journal of Biomedical Informatics
WISB '06 Proceedings of the 2006 workshop on Intelligent systems for bioinformatics - Volume 73
Classification of Mass Spectrometry Based Protein Markers by Kriging Error Matching
MDA '08 Proceedings of the 3rd international conference on Advances in Mass Data Analysis of Images and Signals in Medicine, Biotechnology, Chemistry and Food Industry
Computational prediction models for cancer classification using mass spectrometry data
International Journal of Data Mining and Bioinformatics
IEEE Transactions on Information Technology in Biomedicine
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Hi-index | 3.84 |
Summary: Using replicated human serum samples, we applied an error model for proteomic differential expression profiling for a high-resolution liquid chromatography-mass spectrometry (LC-MS) platform. The detailed noise analysis presented here uses an experimental design that separates variance caused by sample preparation from variance due to analytical equipment. An analytic approach based on a two-component error model was applied, and in combination with an existing data driven technique that utilizes local sample averaging, we characterized and quantified the noise variance as a function of mean peak intensity. The results indicate that for processed LC-MS data a constant coefficient of variation is dominant for high intensities, whereas a model for low intensities explains Poisson-like variations. This result leads to a quadratic variance model which is used for the estimation of sample preparation noise present in LC-MS data.