Data‐independent acquisition mass spectrometry‐based proteomics and software tools: a glimpse in 2020
F Zhang, W Ge, G Ruan, X Cai, T Guo - Proteomics, 2020 - Wiley Online Library
This review provides a brief overview of the development of data‐independent acquisition
(DIA) mass spectrometry‐based proteomics and selected DIA data analysis tools. Various …
(DIA) mass spectrometry‐based proteomics and selected DIA data analysis tools. Various …
Advances in data‐independent acquisition mass spectrometry towards comprehensive digital proteome landscape
RB Kitata, JC Yang, YJ Chen - Mass spectrometry reviews, 2023 - Wiley Online Library
The data‐independent acquisition mass spectrometry (DIA‐MS) has rapidly evolved as a
powerful alternative for highly reproducible proteome profiling with a unique strength of …
powerful alternative for highly reproducible proteome profiling with a unique strength of …
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 …
Mass spectrometry profiling of HLA-associated peptidomes in mono-allelic cells enables more accurate epitope prediction
Identification of human leukocyte antigen (HLA)-bound peptides by liquid chromatography-
tandem mass spectrometry (LC-MS/MS) is poised to provide a deep understanding of rules …
tandem mass spectrometry (LC-MS/MS) is poised to provide a deep understanding of rules …
Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry
We present DeepNovo-DIA, a de novo peptide-sequencing method for data-independent
acquisition (DIA) mass spectrometry data. We use neural networks to capture precursor and …
acquisition (DIA) mass spectrometry data. We use neural networks to capture precursor and …
Mass spectrometry–based identification of MHC-bound peptides for immunopeptidomics
Peptide antigens bound to molecules encoded by the major histocompatibility complex
(MHC) and presented on the cell surface form the targets of T lymphocytes. This critical arm …
(MHC) and presented on the cell surface form the targets of T lymphocytes. This critical arm …
A large fraction of HLA class I ligands are proteasome-generated spliced peptides
The proteasome generates the epitopes presented on human leukocyte antigen (HLA) class
I molecules that elicit CD8+ T cell responses. Reports of proteasome-generated spliced …
I molecules that elicit CD8+ T cell responses. Reports of proteasome-generated spliced …
Towards new horizons: characterization, classification and implications of the tumour antigenic repertoire
SP Haen, MW Löffler, HG Rammensee… - Nature Reviews Clinical …, 2020 - nature.com
Immune-checkpoint inhibition provides an unmatched level of durable clinical efficacy in
various malignancies. Such therapies promote the activation of antigen-specific T cells …
various malignancies. Such therapies promote the activation of antigen-specific T cells …
Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity
M Bassani-Sternberg, C Chong… - PLoS computational …, 2017 - journals.plos.org
The precise identification of Human Leukocyte Antigen class I (HLA-I) binding motifs plays a
central role in our ability to understand and predict (neo-) antigen presentation in infectious …
central role in our ability to understand and predict (neo-) antigen presentation in infectious …
Conventional and neo-antigenic peptides presented by β cells are targeted by circulating naïve CD8+ T cells in type 1 diabetic and healthy donors
S Gonzalez-Duque, ME Azoury, ML Colli, G Afonso… - Cell metabolism, 2018 - cell.com
Summary Although CD8+ T-cell-mediated autoimmune β cell destruction occurs in type 1
diabetes (T1D), the target epitopes processed and presented by β cells are unknown. To …
diabetes (T1D), the target epitopes processed and presented by β cells are unknown. To …