Advancing Proteomic Analyses with Graph-Based Deep Learning: Protein Inference and DIA De Novo Peptide Sequencing

thesis · 2025

thesis · 2025. Zheng Ma
Date 2025-08-15
Type thesis
Publisher PhD thesis
Contribution algorithm
Supervisor Ali Ghodsi
Link https://dspacemainprd01.lib.uwaterloo.ca/server/api/core/bitstreams/2cd3373a-a4cd-4536-8cec-464a86330205/content

Authors

  1. Zheng Ma · University of Waterloo

Methods and tools

  • DIANovo: Transformer-based de novo sequencer for DIA: disentangles coeluted/multiplexed precursor spectra. Presented in Zheng Ma’s arXiv preprint (2024) and his PhD thesis (2025).

Data used

  • A systematic screening pipeline identifies a new regulator of tyrosinated microtubule dynamics (as deposited) · PXD030448
  • An Unbiased Strategy for Selecting Effective Combinations of Therapeutic Targets Supports the Development of a Novel Bis (as deposited) · PXD023034
  • Combined Protein Signature of ALDH1A1, LGALS3, LGALS3BP Predicts Cancer Recurrence Post-Liver Transplantation Beyond Mil (as deposited) · PXD022881
  • Evaluating the influence of MS-acquisition parameters on DDA label-free proteomics analyses (as deposited) · PXD019777
  • Investigation of the arsenic regulated proteome of PML bodies (as deposited) · PXD030330
  • Kinobead profiling of PITCOINs1-3 (as deposited) · PXD032284
  • Narrow-window DIA: Ultra-fast quantitative analysis of comprehensive proteomes with high sequencing depth. Dilution Seri (as deposited) · PXD046283
  • PXD026600 (as deposited) · PXD026600
  • PXD036171 (as deposited) · PXD036171
  • PXD046471 (as deposited) · PXD046471
  • Protein markers in Oral Squamous Cell Carcinoma (OSCC) (as deposited) · PXD025701
  • Proteomics Analysis of Trop2 Xenograft Prostate Tumors (as deposited) · PXD039272
  • Proteomics analysis of amyloid corneal aggregates from lattice corneal dystrophy patients (as deposited) · PXD006640
  • Proteomics investigation of Nucleostemin role in Nucleo-phosmin mutated OCI-AML 3 cell line (as deposited) · PXD034012
  • Response Profiling Using Shotgun Proteomics Enables Establishing Global Metallodrug Mechanisms of Action - cytoplasmic p (as deposited) · PXD004789
  • SARS-CoV-2 ORF8 interactome in the secretory pathway (as deposited) · PXD032035
  • SUPT3H-less SAGA coactivator can assemble and function without significantly perturbing RNA polymerase II transcription (as deposited) · PXD026991
  • Structural analysis of neurofibromin by crosslinking mass spectrometry (as deposited) · PXD023593
  • Targeting the Scaffold Protein Plectin by an Organometallic as a Strategy to Inhibit Tumour Invasive (PXD005388) (as deposited) · PXD005388
  • Targeting the Scaffold Protein Plectin by an Organometallic as a Strategy to Inhibit Tumour Invasiveness- whole cell lys (as deposited) · PXD010319
  • Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-ind (PXD046386) (as deposited) · PXD046386
  • Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-ind (PXD046444) (as deposited) · PXD046444
  • Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition (as deposited) · PXD046453
  • Untargeted data independent acquisition proteomics analysis using Orbitrap mass spectrometers and DIA-Umpire (as deposited) · PXD003179
  • ¬The EGFR/ErbB inhibitor neratinib promotes apoptosis and clearance by airway macrophages (as deposited) · PXD035125

Seen in the charts

Back to the full map

Back to top