Summary The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium
(CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics …

Genomic analyses in cancer have been enormously impactful, leading to the identification of
driver mutations and development of targeted therapies. But the functions of the vast majority …

Liquid chromatography (LC) coupled with data-independent acquisition (DIA) mass
spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we …

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient
survival. Toward understanding the underlying molecular alterations that drive PDAC …

Clear cell renal cell carcinomas (ccRCCs) represent∼ 75% of RCC cases and account for
most RCC-associated deaths. Inter-and intratumoral heterogeneity (ITH) results in varying …

The biological processes that are disrupted in the Alzheimer's disease (AD) brain remain
incompletely understood. In this study, we analyzed the proteomes of more than 1,000 brain …

Lung squamous cell carcinoma (LSCC) remains a leading cause of cancer death with few
therapeutic options. We characterized the proteogenomic landscape of LSCC, providing a …

To explore the biology of lung adenocarcinoma (LUAD) and identify new therapeutic
opportunities, we performed comprehensive proteogenomic characterization of 110 tumors …

Elucidating the wiring diagram of the human cell is a central goal of the postgenomic era.
We combined genome engineering, confocal live-cell imaging, mass spectrometry, and data …

Epigenetic dysregulation is a defining feature of tumorigenesis that is implicated in immune
escape,. Here, to identify factors that modulate the immune sensitivity of cancer cells, we …