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BMCBI
2008

A nonparametric model for quality control of database search results in shotgun proteomics

13 years 3 months ago
A nonparametric model for quality control of database search results in shotgun proteomics
Background: Analysis of complex samples with tandem mass spectrometry (MS/MS) has become routine in proteomic research. However, validation of database search results creates a bottleneck in MS/MS data processing. Recently, methods based on a randomized database have become popular for quality control of database search results. However, a consequent problem is the ignorance of how to combine different database search scores to improve the sensitivity of randomized database methods. Results: In this paper, a multivariate nonlinear discriminate function (DF) based on the multivariate nonparametric density estimation technique was used to filter out false-positive database search results with a predictable false positive rate (FPR). Application of this method to control datasets of different instruments (LCQ, LTQ, and LTQ/FT) yielded an estimated FPR close to the actual FPR. As expected, the method was more sensitive when more features were used. Furthermore, the new method was shown to...
Jiyang Zhang, Jianqi Li, Xin Liu, Hongwei Xie, Yun
Added 09 Dec 2010
Updated 09 Dec 2010
Type Journal
Year 2008
Where BMCBI
Authors Jiyang Zhang, Jianqi Li, Xin Liu, Hongwei Xie, Yunping Zhu, Fuchu He
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