Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1091814 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Vacuoles and lysosomes are single-membrane-bound organelles involved in diverse functions such as intracellular digestion and storage or secretion of metabolites. To understand their origin, evolution and fundamental features, the identification of proteins comprising these compartments in missing links would be invaluable. So, we isolated the vacuoles from Cyanidioschyzon merolae, which is considered to be one of the most primitive photosynthetic eukaryotes, and identified 46 proteins by matrix-assisted laser desorption/ionization time of flight-mass spectrometry. Keywords: peptide mass fingerprinting, MALDI-TOF
2009-09-01 | GSE12042 | GEO
Project description:Chronic infections by hepatitis B virus (HBV) and hepatitis C virus (HCV) appear to be the most significant causes of hepatocellular carcinoma (HCC). Aberrant promoter methylation is known to be deeply involved in cancer, including HCC. In this study, we analyzed aberrant promoter methylation on genome-wide scale in 6 HCCs including 3 HBV-related and 3 HCV-related HCCs, 6 matched noncancerous liver tissues and 3 normal liver tissues by methylated DNA immunoprecipitation-on-chip analysis. Candidate genes with promoter methylation were detected more frequently in HCV-related HCC. Candidate genes methylated preferentially to HBV-related or HCV-related HCCs were detected and selected, and methylation levels of the selected genes were validated using 125 liver tissue samples, including 61 HCCs (28 HBV-related HCCs and 33 HCV-related HCCs) and matched 59 matched noncancerous livers, and 5 normal livers, by quantitative methylation analysis using MALDI-TOF mass spectrometry. Among analyzed genes, preferential methylation in HBV-related HCC was validated in 1 gene only. However, 15 genes were found methylated preferentially in HCV-related HCC, which was independent from age. Hierarchical clustering of HCC using these 15 genes stratified HCV-related HCC as a cluster of frequently methylated samples. The 15 genes included genes inhibitory to cancer-related signaling such as RAS/RAF/ERK and Wnt/b-catenin pathways. It was indicated that genes methylated preferentially in HCV-related HCC exist, and it was suggested that DNA methylation might play an important role in HCV-related HCC by silencing cancer-related pathway inhibitors. we analyzed aberrant promoter methylation in 6 HCC clinical samples (including 3 HBV-related HCCs and 3 HCV-related HCCs) and their matched noncancerous tissues on genome-wide scale by the method. Candidate regions of promoter methylation preferentially to HBV-related HCC and HCV-related HCC were selected, and the methylation levels of these genes were measured quantitatively using MALDI-TOF mass spectrometry. Expression levels of these 6 pairs of HCC and 4 more pairs of HCCs and surrounding noncancerous tissues were analyzed by expression array and are reported in this Series. <br><br>This experiment was reloaded in November 2010 after additional curation. this dataset is part of the TransQST collection.
2010-07-06 | E-GEOD-19665 | biostudies-arrayexpress
Project description:INTRODUCTION: Mass Spectrometry Imaging (MSI) is a hybrid mass spectrometry technique that integrates aspects of traditional microscopy and mass spectrometry-based omics analysis. The traditional MALDI TOF/TOF instrument still remains the dominant platform for this type of anal-ysis. However, with reduced mass resolution compared to other platforms it is insufficient to rely on mass resolution alone for peptide identification. Here we propose a hybrid method of data analysis that integrates both image-based analysis and a parallel protein identification workflow using peptide mass fingerprinting, and its successful application to the detection and validation of viral biomarkers. METHODS: FFPE samples were imaged as described previously in an UltrafleXtreme MALDI TOF/TOF. Total mass spectra were exported and searched against the mouse FASTA da-tabase, while companion images were exported and processed with image J. RESULTS: Peptide mass fingerprinting (PMF) revealed 14 target peptides that were successfully assigned to viral proteins while a pixel based correlational analysis revealed a very high R2 correlation (>0.81) be-tween those same peptides assigned to the NS1 and VP1 viral proteins. CONCLUSIONS: We successfully identified and validated the presence of viral biomarkers to a high degree of confidence using MALDI MSI.
2022-10-13 | PXD034851 | Pride
Project description:Preliminary study of identification of Trichuris suis by MALDI-TOF MS
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Project description:Matrix Selection for the Visualization of Small Molecules and Lipids in Brain Tumors Using Untargeted MALDI-TOF Mass Spectrometry Imaging
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Project description:Cyanobacterial identification by native mass spectrometry
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Project description:Pediatric astrocytomas, a leading cause of death associated with cancer, are the most common primary central nervous system tumors found in children. Most studies of these tumors focus on adults, not children. We examined the global protein and microRNAs expression pattern by 2D SDS-PAGE, mass spectrometry (MALDI-TOF) and RT2 miRNA PCR Array System. MicroRNAs analysis revealed for the first time novel microRNAs involved in astrocytomas biology. Interestingly, miR-138 and miR-145 down-regulation appear to be associated with protein over-expression of vimentin and Bax, respectively. In conclusion, our results show that novel proteins and microRNAs altered on pediatric astrocytoma could serve as biomarkers to distinguish between astrocytoma grades. Astrocytoma samples were colected from patients and total RNA isolation (30 mg of tissue) was performed using the TRIzolM-BM-. protocol (Invitrogen, USA) according to the manufacturerM-bM-^@M-2s instructions. Samples were analyzed using SA Biosciences RT2 miRNA PCRArray System to determied the miRNA expression between control samples and tumors RT2 miRNA PCR Array. Eigth tumor samples and two control tissue (including two control tissue replicates) were used as indicated in the sumary. A total of 3ug of RNA from each tumr samples and control tissue were placed in the PCR Array
2013-02-12 | E-GEOD-44280 | biostudies-arrayexpress
Project description:Identification of different Trichuris spp. using MALDI-TOF MS
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