DeepIso: A Deep Learning Model for Peptide Feature Detection from LC-MS map.
Fatema Tuz ZohoraM Ziaur RahmanNgoc Hieu TranLei XinBaozhen ShanMing LiPublished in: Scientific reports (2019)
Liquid chromatography with tandem mass spectrometry (LC-MS/MS) based quantitative proteomics provides the relative different protein abundance in healthy and disease-afflicted patients, which offers the information for molecular interactions, signaling pathways, and biomarker identification to serve the drug discovery and clinical research. Typical analysis workflow begins with the peptide feature detection and intensity calculation from LC-MS map. We are the first to propose a deep learning based model, DeepIso, that combines recent advances in Convolutional Neural Network (CNN) and Recurrent Neural Network (RNN) to detect peptide features of different charge states, as well as, estimate their intensity. Existing tools are designed with limited engineered features and domain-specific parameters, which are hardly updated despite a huge amount of new coming proteomic data. On the other hand, DeepIso consisting of two separate deep learning based modules, learns multiple levels of representation of high dimensional data itself through many layers of neurons, and adaptable to newly acquired data. The peptide feature list reported by our model matches with 97.43% of high quality MS/MS identifications in a benchmark dataset, which is higher than the matching produced by several widely used tools. Our results demonstrate that novel deep learning tools are desirable to advance the state-of-the-art in protein identification and quantification.
Keyphrases
- deep learning
- convolutional neural network
- tandem mass spectrometry
- liquid chromatography
- artificial intelligence
- neural network
- electronic health record
- ultra high performance liquid chromatography
- mass spectrometry
- machine learning
- big data
- drug discovery
- label free
- high performance liquid chromatography
- ms ms
- simultaneous determination
- high resolution mass spectrometry
- signaling pathway
- end stage renal disease
- newly diagnosed
- loop mediated isothermal amplification
- protein protein
- high intensity
- real time pcr
- spinal cord
- small molecule
- amino acid
- solid phase extraction
- healthcare
- epithelial mesenchymal transition
- single molecule
- wastewater treatment
- endoplasmic reticulum stress
- sensitive detection
- monte carlo