The identification of actionable tumor antigens is indispensable for the development of
several cancer immunotherapies, including T cell receptor–transduced T cells and patient …

Many research questions in fields such as personalized medicine, drug screens or systems
biology depend on obtaining consistent and quantitatively accurate proteomics data from …

The dia-PASEF technology uses ion mobility separation to reduce signal interferences and
increase sensitivity in proteomic experiments. Here we present a two-dimensional peak …

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 …

Abstract Machine learning and in particular deep learning (DL) are increasingly important in
mass spectrometry (MS)-based proteomics. Recent DL models can predict the retention …

MaxDIA is a software platform for analyzing data-independent acquisition (DIA) proteomics
data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves …

We present a proteogenomic study of 108 human papilloma virus (HPV)-negative head and
neck squamous cell carcinomas (HNSCCs). Proteomic analysis systematically catalogs …

Most cancers exhibit aneuploidy, but its functional significance in tumor development is
controversial. Here, we describe ReDACT (Restoring Disomy in Aneuploid cells using …