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E-PROT-69

ABSTRACT: 76 human liver tissue proteomes by PCT-SWATH

PROVIDER: E-PROT-69 | ExpressionAtlas | 2022-01-26

REPOSITORIES: ExpressionAtlas

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Proteomic profiling of NCI60 cell lines from Cancer Cell Line Encyclopedia

Project description: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 (PRIDE) at accession PXD003539 (http://www.ebi.ac.uk/pride/archive/projects/PXD003539). Since the record here does not include the raw data files and hence there is no need to explicitly link individual replicate to a raw file, each sample is only listed once in the ArrayExpress samples table for clarity.

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76 human liver tissue proteomes by PCT-SWATH

Project description:Rapid proteotyping of 38 human liver tissues in duplicate using pressure-cycling technology (PCT) and SWATH mass spectrometry

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ABLE-SWATH - A Case Study and Methodology for OpenSWATH Parameter Optimization Using the ProCan90 Data Set and 45,810 Computational Analysis Runs

Project description: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 substantially reduces the time and cost of tissue sample processing. ABLE is based on pressure cycling technology (PCT) for rapid tissue solubilisation and reliable, controlled proteolytic digestion. Here, the previously reported PCT protocol was optimised using 1-4 mg biopsy punches from rat kidney. The tissue denaturant urea was substituted with a combination of sodium deoxycholate (SDC) and N-propanol. ABLE produced comparable numbers of protein identifications in half the sample preparation time and with reduced cost, being ready for MS injection in 3 hrs (vs the conventional urea PCT method of 6 hrs). To validate the method, it was applied across a diverse range of rat tissues (kidney, lung, muscle, brain, testis), human HEK 293 cells and ovarian tumours by coupling PCT with SWATH-mass spectrometry (SWATH-MS). There were similar numbers of quantified proteins between ABLE-SWATH and PCT-SWATH methods, with greater than 70% overlap for all sample types, except muscle with 58% overlap. The ABLE tissue processing protocol offers a standardised, high-throughput, efficient and reproducible proteomic preparation method, accelerating sample throughput for any type of MS analysis. Coupled with SWATH-MS, ABLE has the potential to accelerate proteomics analysis towards a clinically relevant turn-around-time.

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Project description:PCP39: prostate cancer proteome for 39 patients by PCT-SWATH

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Project description:Comparison of FFPE and fresh frozen prostate tissues using PCT SWATH

2023-11-07 | E-PROT-68 | ExpressionAtlas

PCT-SWATH kidney tissues - Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps

Project description:DDA and SWATH analysis of human kidney tissues. Data set used for PCT-SWATH paper. PCT-SWATH provides the first method to generate a digital map representing the proteome of biopsy level clinical samples from which thousands of proteins can be accurately quantified with a high degree of reproducibility across sample sets.

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E-PROT-73

Project description:NCI60 proteome by PCT-SWATH - Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines

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Project description:Here we investigated the degradation of mRNA and protein in 68 pairs of adjacent prostate tissue samples using RNA-seq and pressure cycling technology (PCT) coupled with SWATH mass spectrometry and developed a score, the Proteome Integrity Number (PIN), to quantify the extent of protein degradation in the samples.

2019-06-12 | PXD007841 | Pride

NCI60 proteome by PCT-SWATH - Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines

Project description: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.

2020-06-01 | PXD003539 | Pride

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