Dataset Information

Deep neural network for detecting arbitrary precision peptide features through attention based segmentation.

ABSTRACT: A promising technique of discovering disease biomarkers is to measure the relative protein abundance in multiple biofluid samples through liquid chromatography with tandem mass spectrometry (LC-MS/MS) based quantitative proteomics. The key step involves peptide feature detection in the LC-MS map, along with its charge and intensity. Existing heuristic algorithms suffer from inaccurate parameters and human errors. As a solution, we propose PointIso, the first point cloud based arbitrary-precision deep learning network to address this problem. It consists of attention based scanning step for segmenting the multi-isotopic pattern of 3D peptide features along with the charge, and a sequence classification step for grouping those isotopes into potential peptide features. PointIso achieves 98% detection of high-quality MS/MS identified peptide features in a benchmark dataset. Next, the model is adapted for handling the additional 'ion mobility' dimension and achieves 4% higher detection than existing algorithms on the human proteome dataset. Besides contributing to the proteomics study, our novel segmentation technique should serve the general object detection domain as well.

SUBMITTER: Zohora FT

PROVIDER: S-EPMC8440683 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

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Deep neural network for detecting arbitrary precision peptide features through attention based segmentation.

Zohora Fatema Tuz FT Rahman M Ziaur MZ Tran Ngoc Hieu NH Xin Lei L Shan Baozhen B Li Ming M

Scientific reports 20210914 1

A promising technique of discovering disease biomarkers is to measure the relative protein abundance in multiple biofluid samples through liquid chromatography with tandem mass spectrometry (LC-MS/MS) based quantitative proteomics. The key step involves peptide feature detection in the LC-MS map, along with its charge and intensity. Existing heuristic algorithms suffer from inaccurate parameters and human errors. As a solution, we propose PointIso, the first point cloud based arbitrary-precision ...[more]

PMID: 34521906

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Dataset Information

Deep neural network for detecting arbitrary precision peptide features through attention based segmentation.

Publications

Deep neural network for detecting arbitrary precision peptide features through attention based segmentation.

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