Stimuli-responsive ferroptosis for cancer therapy
Ferroptosis, an iron-dependent programmed cell death mechanism, is regulated by distinct
molecular pathways of lipid peroxidation caused by intracellular iron supplementation and …
molecular pathways of lipid peroxidation caused by intracellular iron supplementation and …
Decoding post-translational modification crosstalk with proteomics
Post-translational modification (PTM) of proteins allows cells to regulate protein functions,
transduce signals and respond to perturbations. PTMs expand protein functionality and …
transduce signals and respond to perturbations. PTMs expand protein functionality and …
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 …
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 …
[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 …
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 …
Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors
A Kacen, A Javitt, MP Kramer, D Morgenstern… - Nature …, 2023 - nature.com
Post-translational modification (PTM) of antigens provides an additional source of
specificities targeted by immune responses to tumors or pathogens, but identifying antigen …
specificities targeted by immune responses to tumors or pathogens, but identifying antigen …
Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco
Recent advances in methods for enrichment and mass spectrometric analysis of intact
glycopeptides have produced large-scale glycoproteomics datasets, but interpreting these …
glycopeptides have produced large-scale glycoproteomics datasets, but interpreting these …