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ProteomicsProteomic Analysis on Paraffine-Archived Melanoma
The discovery of novel protein biomarkers in melanoma is crucial. Our introduction of formalin-fixed paraffin embedded (FFPE) tumor protocol provides new opportunities to understand the progression of melanoma and open the possibility to screen tens of thousands of FFPE samples deposited in tumor bi...
ORGANISM(S): Homo sapiens (Human) 
2022-02-17 | PXD028930 | Pride
Prognostic and predictive biomarkers Proteomics Metastatic melanoma Immunotherapy targeted therapy responder Outcome and survival by protein expression 
ProteomicsAUTOMATED PHOSPHOPEPTIDE ENRICHMENT FROM MINUTE QUANTITIES OF FROZEN MALIGNANT MELANOMA TISSUE
To acquire a deeper understanding of malignant melanoma (MM), it is essential to study the proteome of patient tissues. In particular, phosphoproteomics of MM has become of significant importance because of the central role that phosphorylation plays in the development of MM. Investigating clinical ...
ORGANISM(S): Homo sapiens (Human) 
2018-11-23 | PXD011175 | Pride
Bravo assaymap Sensitivity Fe(iii)-imac. Malignant melanoma phosphoproteomics Phosphopeptide enrichment 
ProteomicsASSESSING AUTOMATED SAMPLE PREPARATION TECHNOLOGIES FOR HIGH-THROUGHPUT PROTEOMICS OF FROZEN WELL CHARACTERIZED TISSUES FROM SWEDISH BIOBANKS
Large cohorts of carefully collected and stored clinical tissue materials play a central role in acquiring sufficient depth and statistical power to discover disease-related mechanisms and biomarkers of clinical significance. Manual preparation of such heterogeneous samples is labor intensive and re...
ORGANISM(S): Rattus norvegicus (Rat) 
2018-11-27 | PXD011295 | Pride
Mass spectrometry clinical peoteomics 
ProteomicsASSESSING AUTOMATED SAMPLE PREPARATION TECHNOLOGIES FOR HIGH-THROUGHPUT PROTEOMICS OF FROZEN WELL CHARACTERIZED TISSUES FROM SWEDISH BIOBANKS
Large cohorts of carefully collected and stored clinical tissue materials play a central role in acquiring sufficient depth and statistical power to discover disease-related mechanisms and biomarkers of clinical significance. Manual preparation of such heterogeneous samples is labor intensive and re...
ORGANISM(S): Homo sapiens (Human) Rattus norvegicus (Rat) 
2018-11-27 | PXD010296 | Pride
Bravo assaymap Tissue Mass spectrometry Clinical proteomics Barocycler Bioruptor 
ProteomicsProteomic changes linked to the limbic stage of AD
Alzheimer's disease (AD) is a neurodegenerative disorder and the most common cause of dementia worldwide. In AD, neurodegeneration spreads throughout the brain cortex in a gradual and predictable pattern, causing progressive memory decline and cognitive impairment. Here, we conducted proteomic, acet...
ORGANISM(S): Homo sapiens (Human) 
2021-12-30 | PXD027173 | Pride
Neuroinflammation Proteomics Limbic stage Phosphoproteomics Alzheimer's disease 
ProteomicsSample preparation for proteomics
Urea-containing buffer solutions are generally used in proteomic studies to aid protein denaturation and solubilisation during cell and tissue lysis. It is well-known, however, that urea can lead to the carbamylation of peptides and proteins and; subsequently, incomplete digestion of proteins. In...
ORGANISM(S): Rattus rattus (Black rat) Homo sapiens (Human) 
2018-06-06 | PXD009426 | Pride
Lys-c/trypsin Urea Lc-ms/ms 
ProteomicsProteomic workflows for high quality quantitative proteome and PTM analysis of clinically relevant samples from FFPE archives
Well-characterized archival FFPE tissues are of much value for prospective biomarker discovery studies. Protocols that offer high-throughput and good reproducibility are essential in proteomics. Therefore, we developed a workflow implementing efficient paraffin removal and protein extraction from FF...
ORGANISM(S): Homo sapiens (Human) 
2020-12-18 | PXD021986 | Pride
Cancer Lung adenocarcinoma Suspension trapping (s-trap) Lysine acetylation stoichiometry Mass spectrometry Clinical proteomics Ffpe tissue Sample preparation High-throughput Isobaric labeling (tmt) 
ProteomicsProteomic workflows for high quality quantitative proteome and PTM analysis of clinically relevant samples from FFPE archives
Well-characterized archival FFPE tissues are of much value for prospective biomarker discovery studies. Protocols that offer high-throughput and good reproducibility are essential in proteomics. Therefore, we developed a workflow implementing efficient paraffin removal and protein extraction from FF...
ORGANISM(S): Homo sapiens (Human) 
2020-12-18 | PXD021964 | Pride
Cancer Lung adenocarcinoma Suspension trapping (s-trap) Lysine acetylation stoichiometry Mass spectrometry Clinical proteomics Ffpe tissue Sample preparation High-throughput Isobaric labeling (tmt) 
ProteomicsThe Human Melanoma Proteome Atlas – Defining the Molecular Pathology & Complementing the Melanoma Transcriptome
This project is an initiative to map the protein levels in malignant melanoma tumor samples, focused on in-depth histopathology coupled to proteome characterization. The protein levels and localization from this project were determined for a broad spectrum of diverse, surgically isolated melanoma tu...
ORGANISM(S): Homo sapiens (Human) 
2021-07-16 | PXD026086 | Pride
Proteogenomics Histopathology Heterogeneity Braf Phosphorylation Driver mutations Metastatic malignant melanoma Sub-cellular localization Acetylation stoichiometry Post-translational-modification 
ProteomicsClinical proteomics workflow for high quality quantitative proteome and PTM analysis of biologically relevant FFPE tissue samples
In recent years, the use of formalin-fixed paraffin-embedded (FFPE) tissues has increased within cancer research and clinical proteomics. However, the use of FFPE tissues can be demanding due to paraffin embedding and cross-links introduced by the formaldehyde. Here, we developed a workflow implemen...
ORGANISM(S): Homo sapiens (Human) 
2020-12-18 | PXD020157 | Pride
Cancer Suspension trapping Lung adenocarcinoma Mass spectrometry Clinical proteomics Lysine acetylation stoichiomtery Throughput Proteomics Tissue Isobaric labeling Tmt Ffpe Sample preparation S-trap 
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