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ProteomicsCombining data independent acquisition with spike-in SILAC (DIA-SiS) improves proteome coverage and quantification )
Data Independent Acquisition (DIA) is increasingly preferred over Data Dependent Acquisition (DDA) due to its higher throughput and fewer missing values. Whereas DDA often utilizes stable isotope labeling to improve quantification, DIA mostly relies on label-free approaches. Efforts to integrate DIA...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2024-10-14 | PXD052080 | Pride
Multiplexing Dia Plexdia Silac Proteomics Benchmark 
UnknownImproved detection and consistency of RNA-interacting proteomes using DIA SILAC.
Not available
S-EPMC10899761 | biostudies-literature
UnknownCombining Data Independent Acquisition With Spike-In SILAC (DIA-SiS) Improves Proteome Coverage and Quantification.
Not available
S-EPMC11795695 | biostudies-literature
ProteomicsImproved detection and quantitation of RNA-interactome using DIA SILAC
Detection and quantitation of the RNA-interacting proteome is commonly achieved applying SILAC labeling, following by data-dependent acquisition (DDA) of the proteomic data. However, the limited sensitivity of the DDA approach often restricts protein detection to those with higher expression in cell...
ORGANISM(S): Homo sapiens (Human) 
2023-12-19 | PXD045318 | Pride
Hek cells Dia-silac Rna-interactome 
ProteomicsBenchmarking plexDIA analysis with SILAC-labelled Hela cell samples
SILAC labelled Hela cell lysates were mixed in defined ratios and analysed using both DDA and DIA methods, to serve as a benchmark for the novel plexDIA features of DIA-NN.
ORGANISM(S): Homo sapiens (Human) 
2023-10-19 | PXD039578 | Pride
Dia-nn Dia Hela Silac Plexdia 
ProteomicsDIA Spike-in SILAC Revisions; additional submission including single-cell like amounts
Additional data and analyses for submission of DIA-SiS
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2024-10-14 | PXD054343 | Pride
Silac dia benchmark proteomics 
ProteomicsBoxCarmax: a novel high-selectivity data-independent acquisition mass spectrometry method for the analysis of protein turnover and complex samples
The data-independent acquisition (DIA) mode performed in the latest high-resolution, high-speed mass spectrometers offers a powerful analytical tool for biological investigations. The DIA mass spectrometry (MS) combined with the isotopic labeling approach holds a particular promise for increasing th...
ORGANISM(S): Homo sapiens (Human) Rattus norvegicus (Rat) 
2021-02-02 | PXD021922 | Pride
Hela cells Dia Human plasma Serum starvation Pc12 cells 
ProteomicsEvaluation of deep and dynamic proteomic screening strategies at sub-50Hz scan rate and without automation
In this study, we systematically evaluate sample preparation strategies, data acquisition modes and data-analysis approaches for both labeled and label-free proteomics, with the explicit goal of maximizing throughput and quantitative depth using Orbitrap-based instruments operating below 50Hz scan r...
ORGANISM(S): Homo sapiens (Human) 
2026-03-27 | PXD073468 | Pride
ProteomicsImproving SILAC quantification with data independent acquisition to investigate bortezomib-induced protein degradation
Stable isotope labeling by amino acids in cell culture (SILAC) coupled to data-dependent acquisition (DDA) is a common approach to quantitative proteomics with the desirable benefit of reducing batch effects during sample processing and data acquisition. More recently, using data-independent acquisi...
ORGANISM(S): Homo Sapiens 
2022-03-29 | PXD022659 | panorama
ProteomicsIsoform-resolved Correlation Analysis Between mRNA Abundance Dynamics and Protein Level Degradation
We employed an optimized, sensitive DIA-MS method on a high-resolution Orbitrap platform and re-measured the proteomic samples used in a previous study, in which the heterogeneity of HeLa cells across different research labs was analyzed by a multi-omic approach. Using the same MS sample sets of all...
ORGANISM(S): Homo sapiens (Human) 
2020-03-11 | PXD014847 | Pride
Alternative splicing Protein turnover Protein isoform Dia mass spectrometry Correlation analysis Pulsed silac 
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