Comput Biol Chem - ProteinLasso: A Lasso regression approach to protein inference problem in shotgun proteomics.

Tópicos

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Resumo

Protein inference is an important issue in proteomics research. Its main objective is to select a proper subset of candidate proteins that best explain the observed peptides. Although many methods have been proposed for solving this problem, several issues such as peptide degeneracy and one-hit wonders still remain unsolved. Therefore, the accurate identification of proteins that are truly present in the sample continues to be a challenging task. Based on the concept of peptide detectability, we formulate the protein inference problem as a constrained Lasso regression problem, which can be solved very efficiently through a coordinate descent procedure. The new inference algorithm is named as ProteinLasso, which explores an ensemble learning strategy to address the sparsity parameter selection problem in Lasso model. We test the performance of ProteinLasso on three datasets. As shown in the experimental results, ProteinLasso outperforms those state-of-the-art protein inference algorithms in terms of both identification accuracy and running efficiency. In addition, we show that ProteinLasso is stable under different parameter specifications. The source code of our algorithm is available at: http://sourceforge.net/projects/proteinlasso.

Resumo Limpo

protein infer import issu proteom research main object select proper subset candid protein best explain observ peptid although mani method propos solv problem sever issu peptid degeneraci onehit wonder still remain unsolv therefor accur identif protein truli present sampl continu challeng task base concept peptid detect formul protein infer problem constrain lasso regress problem can solv effici coordin descent procedur new infer algorithm name proteinlasso explor ensembl learn strategi address sparsiti paramet select problem lasso model test perform proteinlasso three dataset shown experiment result proteinlasso outperform stateoftheart protein infer algorithm term identif accuraci run effici addit show proteinlasso stabl differ paramet specif sourc code algorithm avail httpsourceforgenetprojectsproteinlasso

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