Proteogenomic data and resources for pan-cancer analysis
Summary The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium
(CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics …
(CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics …
Cancer proteogenomics: current impact and future prospects
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 …
driver mutations and development of targeted therapies. But the functions of the vast majority …
dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts
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 …
increase sensitivity in proteomic experiments. Here we present a two-dimensional peak …
Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform
Liquid chromatography (LC) coupled with data-independent acquisition (DIA) mass
spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we …
spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we …
[HTML][HTML] Proteogenomic characterization of pancreatic ductal adenocarcinoma
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient
survival. Toward understanding the underlying molecular alterations that drive PDAC …
survival. Toward understanding the underlying molecular alterations that drive PDAC …
Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness
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 …
most RCC-associated deaths. Inter-and intratumoral heterogeneity (ITH) results in varying …
[HTML][HTML] A blood atlas of COVID-19 defines hallmarks of disease severity and specificity
DJ Ahern, Z Ai, M Ainsworth, C Allan, A Allcock… - Cell, 2022 - cell.com
Treatment of severe COVID-19 is currently limited by clinical heterogeneity and incomplete
description of specific immune biomarkers. We present here a comprehensive multi-omic …
description of specific immune biomarkers. We present here a comprehensive multi-omic …
Integrated proteogenomic characterization across major histological types of pediatric brain cancer
We report a comprehensive proteogenomics analysis, including whole-genome sequencing,
RNA sequencing, and proteomics and phosphoproteomics profiling, of 218 tumors across 7 …
RNA sequencing, and proteomics and phosphoproteomics profiling, of 218 tumors across 7 …
MSBooster: improving peptide identification rates using deep learning-based features
Peptide identification in liquid chromatography-tandem mass spectrometry (LC-MS/MS)
experiments relies on computational algorithms for matching acquired MS/MS spectra …
experiments relies on computational algorithms for matching acquired MS/MS spectra …
IonQuant enables accurate and sensitive label-free quantification with FDR-controlled match-between-runs
Missing values weaken the power of label-free quantitative proteomic experiments to
uncover true quantitative differences between biological samples or experimental …
uncover true quantitative differences between biological samples or experimental …