Now showing items 1-10 of 10

    • Discovery of New Features for Peptide Sequencing with Mass Spectrometry 

      Wang, Tiancong (University of Waterloo, 2017-09-21)
      Bioinformaticians have been working on peptide sequencing with tandem mass spectrometry (MS/MS) for decades. However, the results are still not perfect. A lot of research have been carried on two peptide sequencing methods, ...
    • Improving Peptide Identification in Proteomics Data Analysis through Repeat-Preserving Decoy and Decoy-Free Retraining 

      Moosa, Johra Muhammad (University of Waterloo, 2024-01-10)
      Accurately identifying peptides in proteomics is central to understanding the complexities of biological systems. Despite the advancements in proteomics data analysis, challenges related to False Discovery Rate (FDR) ...
    • A Machine-Learning-Based Algorithm for Peptide Feature Detection from Protein Mass Spectrometry Data 

      Zeng, Xiangyuan (University of Waterloo, 2021-05-13)
      Liquid chromatography with tandem mass spectrometry (LC-MS/MS) has been widely used in proteomics. Two types of data, MS and MS/MS data, are produced in an LC- MS/MS experiment. The MS data contains signal peaks corresponding ...
    • Mass Spectrometry Based De Novo Peptide Sequencing Error Correction 

      Yao, Chenyu (University of Waterloo, 2017-09-26)
      Extensive study has been conducted on the identification of peptide sequences with mass spectrometry. With the development of computer hardware and algorithms, de novo sequencing has drawn attention from researchers for ...
    • MS/MS Spectrum Prediction for MHC-Associated Peptides with a Fine-Tuned Model 

      Li, Zhenbo (University of Waterloo, 2024-02-23)
      To improve the quality of spectral library search, several MS/MS spectrum predictors have been developed in the last decades. After success in various fields, deep learning techniques are adopted by MS/MS spectrum predictors ...
    • Predicting the Spectrum Quality and Digestive Enzyme for Shotgun Proteomics 

      Gholamizoj, Soroosh (University of Waterloo, 2022-05-03)
      In proteomics, database search programs are routinely used for peptide identification from tandem mass spectrometry data. However, many low-quality spectra cannot be interpreted by any programs. Meanwhile, certain high-quality ...
    • Prediction of AL Amyloidosis Using Deep Learning 

      Murali, Anupa (University of Waterloo, 2023-04-27)
      AL amyloidosis (amyloid light chain or primary amyloidosis) is a rare protein disorder that can be potentially fatal or can cause permanent damage to the organs in the body, especially in cases where the diagnosis does not ...
    • Protein De novo Sequencing 

      Wang, Rong (University of Waterloo, 2016-05-13)
      In the proteomic mass spectrometry field, peptide and protein identification can be classified into two categories: database search that relies on existing peptide and protein databases and de novo sequencing with no prior ...
    • Tagger: Enhance Database Search Tools with De Novo Sequencing Tags 

      Tang, Qi (University of Waterloo, 2017-01-06)
      Tandem mass spectrometry (MS/MS) is widely used in proteomics nowadays to identify peptides and proteins from a sequence database. In a classic procedure of MS/MS protein identification, proteins are digested into short ...
    • A TMT-labeled Spectral Library for Peptide Sequencing 

      Shen, Jianqiao (University of Waterloo, 2017-12-07)
      Tandem mass spectrometry (MS/MS) is widely used nowadays for bioinformaticians to identify peptides and proteins. Three major peptide identification approaches and tools have been developed over the past two decades: ...


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