Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

David Clark, Saravana M. Dhanasekaran, Francesca Petralia, +221

Cell

UrologyGenitourinary CancerKidney ResearchMedicineImmunology +11

Proteogenomic Characterization of Endometrial Carcinoma

Yongchao Dou, Emily Kawaler, Daniel Cui Zhou, +214

Cell

dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts

Vadim Demichev, Łukasz Szyrwiel, Fengchao Yu, +10

Nature Communications

Fast Quantitative Analysis of timsTOF PASEF Data with MSFragger and IonQuant

Fengchao Yu, Sarah E. Haynes, Guo Ci Teo, +3

Molecular & Cellular Proteomics

Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma

Chen Huang, Lijun Chen, Sara R. Savage, +199

Cancer Cell

Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer

Francesca Petralia, Nicole Tignor, Boris Reva, +141

Cell

Identification of modified peptides using localization-aware open search

Fengchao Yu, Guo Ci Teo, Andy T. Kong, +4

Nature Communications

Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco

Daniel A. Polasky, Fengchao Yu, Guo Ci Teo, +1

Nature Methods

GlycoproteomicsBiochemistryMedicineNatural SciencesBioanalysis +6

Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform

Fengchao Yu, Guo Ci Teo, Andy T. Kong, +4

Nature Communications

Fast Deisotoping Algorithm and Its Implementation in the MSFragger Search Engine

Guo Ci Teo, Daniel A. Polasky, Fengchao Yu, +1

Journal of Proteome Research

Cluster ComputingEngineeringAlgorithmic LibraryMolecular BiologyEmpirical Algorithmics +26