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ProteomicsPASS00289 - OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data:SWATH-MS Gold Standard (SGS) Dataset, S. pyogenes Dataset
OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data:SWATH-MS Gold Standard (SGS) Dataset, S. pyogenes Dataset
ORGANISM(S): Streptococcus Pyogenes (ncbitaxon:1314) Saccharomyces Cerevisiae (ncbitaxon:4932) Homo Sapiens (ncbitaxon:9606) 
2017-12-19 | MSV000081829 | MassIVE
ProteomicsThe Pan-Human Library: A repository of assays to quantify 10 000 proteins by SWATH-MS / SWATH-MS validation data
The “Pan-Human Library” is a compendium of highly specific assays covering more than 10 000 human proteins and enabling their targeted analysis in SWATH-MS datasets acquired from research or clinical specimens. This dataset contains validation SWATH-MS data and OpenSWATH results of whole cell lysate...
ORGANISM(S): Homo sapiens (Human) 
2014-08-08 | PXD000954 | Pride
Human Openswath Swath Swath-ms Targeted proteomics Pan-human library 
ProteomicsThe ProCan90 HEK293 dataset - A Case Study and Methodology for OpenSWATH Parameter Optimization Using the ProCan90 Data Set and 45 810 Computational Analysis Runs
A collection of HEK293 SWATH-MS raw data files generated as part of the routine operation of the ProCan experimental facility. These files represent technical replicates each being an aliquot from the same pooled digest, with fifteen runs collected from each of the six Sciex Triple TOF 6600 mass spe...
ORGANISM(S): Homo sapiens (Human) 
2019-04-11 | PXD011093 | Pride
Human Lc-ms Procan 
ProteomicsComparative study of the data analysis tools for data-independent acquisition mass spectrometry
In-house generated datasets of different gradient lengths in comparing the performance of five DIA-MS analysis tools (OpenSWATH, EncyclopeDIA, Skyline, DIA-NN, Spectronaut).
ORGANISM(S): Mus musculus (Mouse) 
2023-08-10 | PXD039759 | Pride
Mouse Liver Swath-ms 
ProteomicsLFQbench enables a multi-centered benchmark study demonstrating robust proteomic label-free quantification
The consistent and accurate quantification of proteins is a challenging task for mass spectrometry (MS)-based proteomics. SWATH-MS uses data-independent acquisition (DIA) for label-free quantification. Here we evaluated five software tools for processing SWATH-MS data: OpenSWATH, SWATH2.0, Skyline, ...
ORGANISM(S): Homo sapiens (Human) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2016-09-27 | PXD002952 | Pride
Lfqbench Lfq Swath-ms Benchmark 
ProteomicsNCI60 proteome by PCT-SWATH - Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines
We obtained quantitative analysis of the NCI-60 cell panels using pressure cycling technology (PCT) and SWATH-MS. Each cell was analyzed in duplicate. The data were analyzed using a cell line SWATH assay library and OpenSWATH, followed by SWATH-expert refinement.
ORGANISM(S): Homo sapiens (Human) 
2020-06-01 | PXD003539 | Pride
Nci-60 cell  pct  swath  breast cancer  luekemia  colon cancer  melanoma  ovarian cancer  brain tumor  renal cancer  lung cancer  prostate cancer  drug sensitivity 
ProteomicsReproducibility, specificity and accuracy of DIA quantification - OpenSWATH
Data dependent acquisition (DDA) is the method of choice for mass spectrometry based proteomics discovery experiments, data-independent acquisition (DIA) is steadily becoming more important. One of the most important requirement to perform a DIA analysis is the availability of spectral libraries for...
ORGANISM(S): Mus musculus (Mouse) 
2019-11-08 | PXD014956 | Pride
Spike-in C2c12 Dia 
ProteomicsProteomic profiling of NCI60 cell lines from Cancer Cell Line Encyclopedia
This ArrayExpress record contains meta-data and results of quantitative analysis of cell lines from the NCI-60 panel using pressure cycling technology (PCT) and SWATH-mass spectrometry. Each cell line was analyzed in duplicate. Raw data files are available at the EMBL-EBI protemics data archive (PRI...
ORGANISM(S): Homo sapiens 
2017-01-27 | E-PROT-2 | biostudies-arrayexpress
ProteomicsABLE-SWATH - A Case Study and Methodology for OpenSWATH Parameter Optimization Using the ProCan90 Data Set and 45,810 Computational Analysis Runs
Proteomic methods typically involve lengthy, multi-step sample preparation protocols (14-16 hrs), especially for the lysis and digestion of solid tissue samples or cells. We developed a streamlined proteomic sample preparation protocol termed Accelerated Barocycler Lysis and Extraction (ABLE), that...
ORGANISM(S): Homo sapiens (Human) Rattus norvegicus (Rat) 
2019-01-21 | PXD010688 | Pride
Urea Sample preparation Clinical proteomics Swath Barocycler Sdc Pct 
ProteomicsEnterococcus faecalis V583, Part 1
Genome-scale models represent the link between an organism's genetic information and experimentally observable biological phenotypes. They facilitate metabolic engineering and the discovery of network properties such as the identification of novel drug targets. Most commonly, metabolite consumption ...
ORGANISM(S): Enterococcus faecalis (Streptococcus faecalis) 
2016-12-06 | PXD001576 | Pride
Swath Ph_shift Efv583 
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