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ProteomicsRobust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel
Single-cell proteomics aims to characterize biological function and heterogeneity at the level of proteins in an unbiased manner. It is currently limited in proteomic depth, throughput, and robustness, which we address here by a streamlined multiplexed workflow using data-independent acquisition (mD...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2022-12-22 | MSV000090956 | MassIVE
ProteomicsDeep Visual Proteomics defines single-cell identity and heterogeneity
Despite the availabilty of imaging-based and mass-spectrometry-based methods for spatial proteomics, a key challenge remains connecting images with single-cell-resolution protein abundance measurements. Here we introduce Deep Visual Proteomics (DVP), which combines artificial-intelligence-driven ima...
ORGANISM(S): Homo sapiens (Human) 
2022-04-27 | PXD023904 | Pride
Microscopy Digital pathology Proteomics Laser microdissection 
ProteomicsParallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF)
Data independent acquisition modes isolate and concurrently fragment populations of different precursors by cycling through segments of a predefined precursor m/z range. Although these selection windows collectively cover the entire m/z range, overall only a few percent of all incoming ions in each ...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2020-12-17 | PXD017703 | Pride
Tims Pasef Dia Technical Ion mobility 
ProteomicsPervasive functional micropeptides in humans encoded by non-canonical open reading frames
Protein-coding regions of the genome continue to expand beyond canonical annotations and remain incompletely understood. Despite recent reports demonstrating important cellular functions played by micropeptides from unannotated open reading frames (ORFs), there exists no systematic method to fully u...
ORGANISM(S): Homo sapiens (Human) 
2020-03-06 | PXD014031 | Pride
Novel orfs Single cell rna analysis Crispr Ribosome sequencing Lcms 
ProteomicsRobust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel
Single-cell proteomics aims to characterize biological function and heterogeneity at the level of proteins in an unbiased manner. It is currently limited in proteomic depth, throughput, and robustness, which we address here by a streamlined multiplexed workflow using data-independent acquisition (mD...
ORGANISM(S): Homo sapiens (Human) 
2023-08-30 | PXD038632 | Pride
Mass spectrometry Dimethyl labeling Multiplexing Dia Single cells 
ProteomicsRapid and in-depth coverage of the (phospho-)proteome with deep libraries and optimal window design for dia-PASEF
Data-independent acquisition (DIA) methods have become increasingly attractive in mass spectrometry (MS)-based proteomics, because they enable high data completeness and a wide dynamic range. Recently, we combined DIA with parallel accumulation – serial fragmentation (dia-PASEF) on a Bruker trapped ...
ORGANISM(S): Homo sapiens (Human) 
2022-08-11 | PXD034128 | Pride
Pasef Egf Tims Data-independent acquisition Phosphoproteomics Systems biology 
UnknownImproving precision for detecting change in the shape of the cornea in patients with keratoconus.
Not available
S-EPMC6097997 | biostudies-literature
ProteomicsA standardized and reproducible workflow for membrane glass slides in routine histology and spatial proteomics
Defining the molecular phenotype of single cells in-situ is essential for understanding tissue heterogeneity in health and disease. Powerful imaging technologies have recently been joined by spatial omics technologies, promising unparalleled insights into the molecular landscape of biological sample...
ORGANISM(S): Homo sapiens (Human) 
2023-10-24 | PXD040281 | Pride
Antigen retrieval Spatial proteomics Deep visual proteomics Glycerol Membrane slides Histology Proteomics Heat-induced epitope retrieval Laser microdissection 
ProteomicsThe social and structural architecture of the yeast protein interactome
Nearly all cellular functions are mediated by protein-protein interactions and mapping the interactome provides fundamental insights into the regulation and structure of biological systems. In principle, affinity purification coupled to mass spectrometry (APMS) is an ideal and scalable tool, however...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2023-09-11 | PXD031940 | Pride
Ae-ms Pasef Pull-downs Saccharomyces cerevisiae Ap-ms Interactome Timstof pro Quantitative interactomics 
ProteomicsOnline parallel accumulation – serial fragmentation (PASEF) with a novel trapped ion mobility mass spectrometer
In bottom-up proteomics, peptides are separated by liquid chromatography with elution peak widths in the range of seconds, while mass spectra are acquired in about 100 microseconds with time-of-fight (TOF) instruments. This allows adding ion mobility as a third dimension of separation. Among several...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2018-11-06 | PXD010012 | Pride
Tims Pasef Technological 
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