Advances and utility of the human plasma proteome
The study of proteins circulating in blood offers tremendous opportunities to diagnose,
stratify, or possibly prevent diseases. With recent technological advances and the urgent …
stratify, or possibly prevent diseases. With recent technological advances and the urgent …
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 …
[HTML][HTML] 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 …
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation
AD Brunner, M Thielert, C Vasilopoulou… - Molecular systems …, 2022 - embopress.org
Single‐cell technologies are revolutionizing biology but are today mainly limited to imaging
and deep sequencing. However, proteins are the main drivers of cellular function and in …
and deep sequencing. However, proteins are the main drivers of cellular function and in …
Increasing the throughput of sensitive proteomics by plexDIA
Current mass spectrometry methods enable high-throughput proteomics of large sample
amounts, but proteomics of low sample amounts remains limited in depth and throughput. To …
amounts, but proteomics of low sample amounts remains limited in depth and throughput. To …
[HTML][HTML] Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition
Mass spectrometry (MS)-based proteomics aims to characterize comprehensive proteomes
in a fast and reproducible manner. Here we present the narrow-window data-independent …
in a fast and reproducible manner. Here we present the narrow-window data-independent …
[HTML][HTML] 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 …
[HTML][HTML] Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance
Microbial communities are composed of cells of varying metabolic capacity, and regularly
include auxotrophs that lack essential metabolic pathways. Through analysis of auxotrophs …
include auxotrophs that lack essential metabolic pathways. Through analysis of auxotrophs …
Making single-cell proteomics biologically relevant
Recent technological advances in mass spectrometry promise to add single-cell proteomics
to the biologist's toolbox. Here we discuss the current status and what is needed for this …
to the biologist's toolbox. Here we discuss the current status and what is needed for this …
[HTML][HTML] Time-resolved in vivo ubiquitinome profiling by DIA-MS reveals USP7 targets on a proteome-wide scale
M Steger, V Demichev, M Backman, U Ohmayer… - Nature …, 2021 - nature.com
Mass spectrometry (MS)-based ubiquitinomics provides system-level understanding of
ubiquitin signaling. Here we present a scalable workflow for deep and precise in vivo …
ubiquitin signaling. Here we present a scalable workflow for deep and precise in vivo …