Journal Article10.1021/JASMS.0C00254
Phenotype Classification using Proteome Data in a Data-Independent Acquisition Tensor Format.
Fangfei Zhang,Shaoyang Yu,Shaoyang Yu,Lirong Wu,Zelin Zang,Xiao Yi,Jiang Zhu,Cong Lu,Ping Sun,Yaoting Sun,Sathiyamoorthy Selvarajan,Lirong Chen,X D Teng,Yongfu Zhao,Guangzhi Wang,Junhong Xiao,Shiang Huang,Oi Lian Kon,N. Gopalakrishna Iyer,Stan Z. Li,Zhongzhi Luan,Tiannan Guo +21 more
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TL;DR: A new strategy for DIA data analysis based on a novel data format called DIAT, which enables facile two-dimensional visualization of DIA proteomics data, and surpassed the deep-learning model based on peptide and protein matrices generated by OpenSWATH.
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About: This article is published in Journal of the American Society for Mass Spectrometry. The article was published on 26 Oct 2020.
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Citations
Deep learning neural network tools for proteomics
Jesse G. Meyer
- 21 Jun 2021
TL;DR: This review summarizes the recent flurry of machine-learning strategies using artificial deep neural networks (or “deep learning”) that have started to break barriers and accelerate progress in the field of shotgun proteomics.
77
Artificial intelligence defines protein-based classification of thyroid nodules
Yaoting Sun,Sathiyamoorthy Selvarajan,Zelin Zang,Wei Li,Yi Zhu,Hao Zhang,Wanyuan Chen,Hao Chen,Lu Li,X. Cai,Huanhuan Gao,Zhicheng Wu,Yongfu Zhao,Lirong Chen,Xiaodong Teng,Sangeeta Mantoo,Tony Kiat Hon Lim,Bhuvaneswari Hariraman,Serene Dingju Yeow,Syed Muhammad Fahmy Alkaff,Sze Sing Lee,Guan Ruan,Qiushi Zhang,Tiansheng Zhu,Yifan Hu,Zhengbang Dong,Weigang Ge,Qi Xiao,Weibin Wang,Guangzhi Wang,Junhong Xiao,Yi He,Zhihong Wang,Wei Sun,Yuan Qin,Jing Zhu,Xu Zheng,Linyan Wang,Xi Zheng,Kailun Xu,Yingkuan Shao,Shu Zheng,Kexin Liu,Ruedi Aebersold,Haixia Guan,Xiao-Hua Wu,Dingcun Luo,Wen Tian,Stan Z. Li,Oi Lian Kon,N. Gopalakrishna Iyer,Tiannan Guo +51 more
TL;DR: In this paper , an AI-defined protein-based biomarker panel for diagnostic classification of thyroid nodules was developed. But the authors did not consider fine-needle aspiration (FNA) tissue specimens of minute amounts.
Acquisition and analysis of DIA-based proteomic data: a comprehensive survey in 2023.
Ronghui Lou,Wenqing Shui +1 more
TL;DR: A comprehensive overview of recent advances in both the experimental and computational methods for DIA proteomics, from data acquisition schemes to analysis strategies and software tools is provided.
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Rapid Screening of COVID-19 Directly from Clinical Nasopharyngeal Swabs Using the MasSpec Pen.
Kyana Y. Garza,Alex Ap Rosini Silva,Jonas R Rosa,Michael F Keating,Sydney C Povilaitis,Meredith Spradlin,Pedro H Godoy Sanches,Alexandre Varao Moura,Junier Marrero Gutierrez,John Q. Lin,Jialing Zhang,Rachel J. DeHoog,Alena Bensussan,Sunil Badal,Danilo Cardoso de Oliveira,Pedro Henrique Dias Garcia,Lisamara Dias de Oliveira Negrini,Marcia Ap Antonio,Thiago C. Canevari,Marcos N. Eberlin,Robert Tibshirani,Livia S. Eberlin,Andreia M Porcari +22 more
TL;DR: In this article, the MasSpec Pen technology integrated to electrospray ionization (ESI) was used for direct analysis of clinical swabs and investigate its use for COVID-19 screening.
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Proteome Landscapes of Human Hepatocellular Carcinoma and Intrahepatic Cholangiocarcinoma.
Xiaoli Yi,Jiang Zhu,Wei Li,Li Peng,Cong Lu,Ping Sun,Lingling Huang,Xiu Nie,Shiang Huang,Tiannan Guo,Yi Zhu +10 more
TL;DR: Wang et al. as mentioned in this paper characterized the proteome landscapes of hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (CCA) using the data independent acquisition (DIA) mass spectrometry (MS) method.
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