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ProteomicsA hybrid DDA/DIA-PASEF based assay library for a deep proteotyping of triple-negative breast cancer
Generation of a new library of targeted mass spectrometry assays for accurate protein quantification in triple negative breast cancer (TNBC) tissues. Primary tumor tissue lysates from 105 TNBC patients treated at Masaryk Memorial Cancer Institute (MMCI) in Brno, Czech Republic, were used to generate...
ORGANISM(S): Homo sapiens (Human) 
2024-05-31 | PXD047793 | Pride
Proteomics Mass spectrometry Data independent acquisition Assay library Triple-negative breast cancer 
MetabolomicsDIAMetAlyzer allows automated false-discovery rate-controlled analysis for data-independent acquisition in metabolomics
The extraction of meaningful biological knowledge from high-throughput mass spectrometry data relies on limiting false discoveries to a manageable amount. For targeted approaches in metabolomics a main challenge is the detection of false positive metabolic features in the low signal-to-noise ranges ...
2022-09-05 | MTBLS1108 | MetaboLights
ProteomicsCavia porcellus spectral library
The guinea pig (cavia porcellus) is an excellent experimental model for translation to many aspects of human physiology and disease yet there is limited experimental information regarding its proteome. In an effort to overcome this gap in our knowledge, we generated a comprehensive spectral library ...
ORGANISM(S): Cavia Porcellus (ncbitaxon:10141) 
2018-12-07 | MSV000083199 | MassIVE
MetabolomicsMetabolome and comparative genome provide insights into secondary metabolites generation of a rare karst-growing Rhododendron in vitro culture

Rhododendron species have the potential to be rich in secondary metabolites with pharmaceutical or industrial value. However, there is a lack of in comprehensive metabolome studies at the genome level, particularly for unique and rare species like R. bailiense which exclusively grows in karst env...

2025-01-02 | MTBLS11581 | MetaboLights
ProteomicsDeep proteome coverage of microglia using a streamlined data independent acquisition-based proteomic workflow: method consideration for a phenotypically diverse cell type
As the immune cells of the brain, microglia play a key role in various homeostatic and disease-related processes. In order to carry out their numerous functions, microglia are able to adopt a wide range of phenotypic states. The proteomic landscape represents a more accurate molecular representation...
ORGANISM(S): Mus musculus (Mouse) 
2025-03-31 | PXD056436 | Pride
Dia-pasef Dda library generation Deep proteomics Microglia Dia methods development 
ProteomicsComprehensive Proteomics Profiling of Zebrafish Retina Using a Hybrid DDA/DIA-PASEF Spectral Library on a timsTOF Pro 2 Mass Spectrometer
The zebrafish (Danio rerio) retina has been increasingly used for studying vertebrate visual processing and ocular growth regulation as it has a high anatomical and physiological similarity to the human eye. Recently, the integration of trapped ion mobility spectrometry (TIMS) with parallel accumula...
ORGANISM(S): Danio rerio (Zebrafish) (Brachydanio rerio) 
2026-06-17 | PXD076440 | Pride
Dia Retina Zebrafish Dda 
ProteomicsA new mass spectral library for high-coverage and reproducible analysis of the Plasmodium falciparum-infected red blood cell proteome
Background: Plasmodium falciparum causes the majority of malaria mortality worldwide, and the disease occurs during the asexual red blood cell (RBC) stage of infection. In the absence of an effective and available vaccine, and with increasing drug resistance, asexual RBC stage parasites are an impor...
ORGANISM(S): Homo sapiens (Human) Plasmodium falciparum 
2021-08-06 | PXD027241 | Pride
Malaria Dia Plasmodium falciparum Spectral library 
ProteomicsA new mass spectral library for high-coverage and reproducible analysis of the Plasmodium falciparum-infected red blood cell proteome
Background: Plasmodium falciparum causes the majority of malaria mortality worldwide, and the disease occurs during the asexual red blood cell (RBC) stage of infection. In the absence of an effective and available vaccine, and with increasing drug resistance, asexual RBC stage parasites are an impor...
ORGANISM(S): Homo sapiens (Human) Plasmodium falciparum 
2021-11-15 | PXD027301 | Pride
Plasmodium falciparum Malaria Dia Spectral library 
ProteomicsA large-scale assay library for targeted protein quantification in renal cell carcinoma tissues
Generation of a new library of targeted mass spectrometry assays for accurate protein quantification in malignant and normal kidney tissue. Aliquots of primary tumor tissue lysates from 86 patients with initially localized renal cell carcinoma (RCC), 75 patients with metastatic RCC treated with suni...
ORGANISM(S): Homo sapiens (Human) 
2022-01-03 | PXD028411 | Pride
Data independent acquisition Targeted proteomics Assay library Spectral library Renal cancer Selected reaction monitoring 
ProteomicsApplication of the HCC spectral library in DIA quantitation
This project stores the search results of MaxQuant2.0.3.0 of 162 HCC cell line raw files and 48 raw files for spectral library generation, and search results of DIA-NN version 1.8 and Spectronaut version15.2 of HepG2, HCCLM3 and TGFB1-stimulated HCCLM3.
ORGANISM(S): Homo sapiens (Human) 
2022-11-11 | PXD037159 | Pride
Hcc celllines hepg2 hcclm3 tgfb1 dia 
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