OmicsEV: a tool for comprehensive quality evaluation of omics data tables

Article Multidisciplinary Sciences

Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity

Klemens Froehlich et al.

Summary: This study presents a benchmark dataset for evaluating DIA data analysis workflows in clinical settings, using real-world inter-patient heterogeneity. The results demonstrate the effectiveness of gas-phase fractionated spectral libraries and non-parametric permutation-based statistical tests for correctly identifying differentially abundant proteins in DIA analysis.

NATURE COMMUNICATIONS (2022)

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Article Oncology

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

Chen Huang et al.

Summary: This study presents a proteogenomic analysis of HPV-negative HNSCCs, identifying potential therapeutic targets and uncovering tumor characteristics such as immune status and resistance mechanisms. The findings suggest new strategies for stratifying HNSCC and improving treatment outcomes.

CANCER CELL (2021)

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Article Biochemistry & Molecular Biology

Proteogenomic characterization of pancreatic ductal adenocarcinoma

Liwei Cao et al.

Summary: This study conducted comprehensive proteogenomic analysis of PDAC to understand the molecular alterations that drive oncogenesis. Multiple analyses were performed on tissues from patients, providing valuable resources for early detection and identification of therapeutic targets.

CELL (2021)

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Article Biochemistry & Molecular Biology