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author:("Lin, wendun")
1.  An unsupervised machine learning method for assessing quality of tandem mass spectra 
Proteome Science  2012;10(Suppl 1):S12.
Background
In a single proteomic project, tandem mass spectrometers can produce hundreds of millions of tandem mass spectra. However, majority of tandem mass spectra are of poor quality, it wastes time to search them for peptides. Therefore, the quality assessment (before database search) is very useful in the pipeline of protein identification via tandem mass spectra, especially on the reduction of searching time and the decrease of false identifications. Most existing methods for quality assessment are supervised machine learning methods based on a number of features which describe the quality of tandem mass spectra. These methods need the training datasets with knowing the quality of all spectra, which are usually unavailable for the new datasets.
Results
This study proposes an unsupervised machine learning method for quality assessment of tandem mass spectra without any training dataset. This proposed method estimates the conditional probabilities of spectra being high quality from the quality assessments based on individual features. The probabilities are estimated through a constraint optimization problem. An efficient algorithm is developed to solve the constraint optimization problem and is proved to be convergent. Experimental results on two datasets illustrate that if we search only tandem spectra with the high quality determined by the proposed method, we can save about 56 % and 62% of database searching time while losing only a small amount of high-quality spectra.
Conclusions
Results indicate that the proposed method has a good performance for the quality assessment of tandem mass spectra and the way we estimate the conditional probabilities is effective.
doi:10.1186/1477-5956-10-S1-S12
PMCID: PMC3380733  PMID: 22759570
2.  Features-Based Deisotoping Method for Tandem Mass Spectra 
Advances in Bioinformatics  2012;2011:210805.
For high-resolution tandem mass spectra, the determination of monoisotopic masses of fragment ions plays a key role in the subsequent peptide and protein identification. In this paper, we present a new algorithm for deisotoping the bottom-up spectra. Isotopic-cluster graphs are constructed to describe the relationship between all possible isotopic clusters. Based on the relationship in isotopic-cluster graphs, each possible isotopic cluster is assessed with a score function, which is built by combining nonintensity and intensity features of fragment ions. The non-intensity features are used to prevent fragment ions with low intensity from being removed. Dynamic programming is adopted to find the highest score path with the most reliable isotopic clusters. The experimental results have shown that the average Mascot scores and F-scores of identified peptides from spectra processed by our deisotoping method are greater than those by YADA and MS-Deconv software.
doi:10.1155/2011/210805
PMCID: PMC3259476  PMID: 22262971

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