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ProteomicsReprocessed dataset with Skyline Batch: Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen treated 3D liver microtissues
The data set represents a fair comparison of shotgun proteomics with HRM (swath type DIA). Additionally, a human liver microtissue was profiled with HRM. REPROCESSING METHODS: Skyline Batch is a newly developed Windows forms application that enables easy and consistent reprocessing of data with Skyl...
ORGANISM(S): Homo Sapiens 
2021-11-12 | PXD029663 | panorama
ProteomicsReprocessed dataset with Skyline Batch: SWATH Analysis of Yeast Proteome over Time in Response to Osmotic Stress
SWATH analysis of Yeast Proteome over time in response to Osmotic Stress. We sampled cell cultures in biological triplicates at six time points following the application of osmotic stress and acquired single injection DIA datasets on a high-resolution 5600 tripleTOF instrument operated in SWATH mode...
ORGANISM(S): Saccharomyces Cerevisiae 
2021-11-12 | PXD029665 | panorama
ProteomicsComprehensive peptide quantification for data independent acquisition mass spectrometry using chromatogram libraries
Raw DDA and DIA data to support Searle et al. 2018. Comprehensive peptide quantification for data independent acquisition mass spectrometry using chromatogram libraries. bioRxiv doi:10.1101/277822
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Saccharomyces Cerevisiae (ncbitaxon:4932) 
2018-08-08 | MSV000082805 | MassIVE
ProteomicsDeepMRM: targeted proteomics data interpretation package with deep learning-based object detection
LC-MRM-MS/MS data of 66 Pancreatic ductal adenocarcinoma patients. Includes peak list files (.mzML), quantification results (.tsv) and raw files (.d) of the three replicate data of all patients.
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2022-07-19 | MSV000089914 | MassIVE
ProteomicsPeptide centric detection of cross-linked peptides using PASEF, MeroX, and Skyline
Cross-linking mass spectrometry (XL-MS) has evolved into a pivotal technique for probing protein interactions, with recent ad-vancements significantly enhancing its analytical potential. This technical note presents advancements in cross-linking mass spec-trometry (XL-MS) through the implementation ...
ORGANISM(S): Bos Taurus 
PXD047307 | panorama
ProteomicsQuantitative XL-MS Analysis of HHARI in the presence or absence of 4EHP
RING-Between-RING (RBR) E3 ligases mediate ubiquitin transfer through an obligate E3- ubiquitin thioester intermediately prior to substrate ubiquitination. While RBRs share a conserved catalytic module, substrate recruitment mechanisms remain enigmatic and the relevant domains have yet to be identi...
ORGANISM(S): Homo Sapiens 
PXD030871 | panorama
ProteomicsCarafe enables high quality in silico spectral library generation for data-independent acquisition proteomics
Data-independent acquisition (DIA)-based mass spectrometry is becoming an increasingly popular mass spectrometry acquisition strategy for carrying out quantitative proteomics experiments. Most of the popular DIA search engines make use of in silico generated spectral libraries. However, the generati...
ORGANISM(S): Homo Sapiens Saccharomyces Cerevisiae 
2025-11-09 | PXD056793 | panorama
ProteomicsA framework for quality control in quantitative proteomics
A thorough evaluation of the quality, reproducibility, and variability of bottom-up proteomics data is necessary at every stage of a workflow, from planning to analysis. We share vignettes applying adaptable quality control (QC) measures to assess sample preparation, system function, and quantitativ...
ORGANISM(S): Homo Sapiens Mus Musculus Bos Taurus Saccharomyces Cerevisiae 
PXD051318 | panorama
ProteomicsEvaluation of a modified Orbitrap Astral Zoom prototype for quantitative proteomics - Beyond identification lists
Mass spectrometry instrumentation continues to evolve rapidly, yet quantifying these advances beyond conventional peptide and protein detections remains challenging. Here, we evaluate a modified Orbitrap Astral Zoom mass spectrometer (MS) prototype and compare its performance to the standard Orbitra...
ORGANISM(S): Homo Sapiens Gallus Gallus 
PXD064536 | panorama
ProteomicsEvaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data Independent Acquisition
We evaluate the quantitative performance of the newly released Asymmetric Track Lossless (Astral) analyzer. Using data independent acquisition, the Orbitrap Astral mass spectrometer quantifies 5 times more peptides per unit time than state-of-the-art Orbitrap mass spectrometers, which have long been...
ORGANISM(S): Homo Sapiens 
PXD042704 | panorama
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