apQuant: Accurate Label-Free Quantification by Quality Filtering

被引：57

作者：

Doblmann, Johannes ^{[1
]}

Dusberger, Frederico ^{[1
]}

Imre, Richard ^{[1
,2
]}

Hudecz, Otto ^{[1
,2
]}

Stanek, Florian ^{[1
]}

Mechtler, Karl ^{[1
,2
]}

Duernberger, Gerhard ^{[1
,2
,3
]}

机构：

[1] Vienna Bioctr VBC, Res Inst Mol Pathol IMP, Campus Vienna Bioctr 1, A-1030 Vienna, Austria

[2] Vienna Bioctr VBC, Austrian Acad Sci IMBA, Inst Mol Biotechnol, Dr Bohr Gasse 3, A-1030 Vienna, Austria

[3] Vienna Bioctr VBC, Gregor Mendel Inst Mol Plant Biol GMI, Dr Bohr Gasse 3, A-1030 Vienna, Austria

来源：

JOURNAL OF PROTEOME RESEARCH | 2019年 / 18卷 / 01期

基金：

奥地利科学基金会;

关键词：

quantitative proteomics; mass spectrometry; label-free quantification; data analysis pipeline; computational proteomics; PEPTIDE IDENTIFICATION; MASS; PLATFORM; DRAFT; TOOL;

D O I：

10.1021/acs.jproteome.8b00113

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Label-free quantification of shotgun proteomics data is a frequently used strategy, offering high dynamic range, sensitivity, and the ability to compare a high number of samples without additional labeling effort. Here, we present a bioinformatics approach that significantly improves label-free quantification results. We employ Percolator to assess the quality of quantified peptides. This allows to extract accurate and reliable quantitative results based on false discovery rate. Benchmarking our approach on previously published public data shows that it considerably outperforms currently available algorithms. apQuant is available free of charge as a node for Proteome Discoverer.

引用

页码：535 / 541

页数：7

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