MALDI-FTICR-MS total plasma N-glycomics
Ontology highlight
ABSTRACT:
INSTRUMENT(S): apex ultra
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: Manfred Wuhrer
PROVIDER: MSV000080307 | MassIVE | Wed Nov 02 07:45:00 GMT 2016
REPOSITORIES: MassIVE
Similar Datasets
Project description:Glycosylation is the most common post-translational modification of proteins, yet genes relevant to the synthesis of glycan structure and function are incompletely represented and poorly annotated on the commercially available arrays. To fill the need for expression analysis of such genes we employed the Affymetrix technology to develop a focused and highly annotated glycogene chip representing human and murine glycogenes, including glycosyltranferases, nucleotide sugar transporters, glycosidases, proteoglycans and glycan-binding proteins. In this report the array has been used to generate glycogene expression profiles of nine murine tissues. Global analysis with a hierarchical clustering algorithm, reveals that expression profiles in immune tissues (thymus, spleen, lymph node and bone marrow) are more closely related, relative to those of non-immune tissues (kidney, liver, brain and testes). Of the biosynthetic enzymes, those responsible for synthesis of the core regions of N-and O-linked oligosaccharides are ubiquitously expressed, while glycosyltransferase that elaborate terminal structures are expressed in a highly tissue-specific manner, accounting for tissue and ultimately cell type-specific glycosylation. Comparison of gene expression profiles with MALDI-TOF profiling of N-linked oligosaccharides suggested that the alpha-1-3 fucosyltransferase IX, Fut9, is the enzyme responsible for terminal fucosylation in kidney and brain, a finding validated by analysis of Fut9 knockout mice. Two families of glycan-binding proteins, C-type lectins and siglecs, are predominately expressed in the immune tissues, consistent with their emerging functions in both innate and acquired immunity. The glycogene chip reported in this study is available to the scientific community through the Consortium for Functional Glycomics (http://www.functionalglycomics.org). Keywords: Glycogenes, Glycomics, Glycosyltransferase, Lectin, Glycosylation, Glycome, Microarray, Kidney, Fut9
2005-06-20 | GSE2781 | GEO
Project description:MALDI-imaging-guided Transcriptomics
| PRJEB69276 | ENA
Project description:Advances in high-throughput molecular analyses of collagen peptides, especially ZooMS (Zooarchaeology by Mass Spectrometry), have addressed the issue of intense skeletal fragmentation at Palaeolithic archaeological sites, which hinders morphological identification. However, the challenge of variable collagen preservation persists. We aim to evaluate the potential of two mass analyzers TOF vs FTICR to propose novel options to enhance the ZooMS workflow. Type 1 collagen (COL1) was extracted from 89 archaeological bones from the site of Le Piage (France, 37-34 ka cal BP). Three distinct ZooMS protocols were used: an acid-free method (AmBic) and two demineralizations (HCl and TFA), combined with MALDI-TOF and MALDI-FTICR instruments. The first offers rapid and cheap analysis, while the second provides higher resolution. Taxonomic identifications were made by peptide mass fingerprinting (PMF). Finally, LC-MS/MS was applied to verify 26 low-collagen samples identifications.
2025-03-17 | PXD056898 | Pride
Project description:Intestinal ischemia-reperfusion injury (IR) is a severe clinical condition, and unraveling its pathophysiology is crucial in order to improve therapeutic strategies and reduce the high morbidity and mortality rates. Here, we studied the dynamic proteome and phosphoproteome in human intestine during ischemia and reperfusion, using LC-MS analysis to gain quantitative information of thousands of proteins and phosphosites, as well as MS imaging to obtain spatial information. We identified a significant decrease in abundance of proteins related to intestinal absorption, microvillus and cell junction, whereas proteins involved in innate immunity, in particular the complement cascade, and extracellular matrix organization increased in abundance after IR. Differentially phosphorylated proteins were involved in RNA splicing events and cytoskeletal and cell junction organization. In addition, our analysis points to MAPK and CDK families to be active kinases during IR. Finally, MALDI-TOF MS imaging presented peptide alterations in abundance and distribution, which resulted, in combination with FTICR-MS imaging and LC-MS, in the identification of additional proteins related to RNA splicing, the complement cascade and extracellular matrix organization. This study expanded our understanding of the molecular changes that occur during IR in human intestine, and highlights the value of the complementary use of different MS-based methodologies.
2022-11-08 | PXD026076 | Pride
Project description:Identification of different Trichuris spp. using MALDI-TOF MS
| PRJEB50468 | ENA
Project description:More than 50% of all known proteins are glycosylated, which is critical for many biological processes such as protein folding and signal transduction. Glycosylation has proven to be associated with different mammalian diseases such as breast and liver cancers. Therefore, characterization of glycans is highly important to facilitate a better understanding of the development and progression of many human diseases. Although matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) offers several advantages such as ease of operation and short analysis times, however, due to the complexity of glycan structures and their low ionization efficiency, there are still challenges that need to be addressed to achieve sensitive glycan analysis. Here, magnetic carbon nanocomposites (CNPs@Fe3O4 NCs) were used as a new MALDI matrix or co-matrix for the analysis of glycans derived from different model glycoproteins and human blood serum samples. The addition of CNPs@Fe3O4 NCs to the matrix significantly enhanced glycan signal intensity by several orders of magnitude, and effectively controlled/reduced/eliminated in-source decay (ISD) fragmentation. The latter was attained by modulating CNPs@Fe3O4 NCs concentrations and allowed the simultaneous study of intact and fragmented glycans, and pseudo-MS3 analysis. Moreover, CNPs@Fe3O4 NCs was also effectively employed to desalt samples directly on MALDI plate, thus enabling direct MALDI-MS analysis of unpurified permethylated glycans derived from both model glycoproteins and biological samples. On-plate desalting enhanced sensitivity by reducing sample loss. Graphical abstract ᅟ.
| S-EPMC6375713 | biostudies-literature
Project description:MALDI-TOF_serum_metabolome
2023-05-25 | OEX00023764 | NODE
Project description:High-mass-resolution imaging mass spectrometry promises to localize hundreds of metabolites directly from tissues, cell cultures, and agar plates with cellular resolution, but is hampered by the lack of bioinformatics for automated metabolite identification. We developed the first bioinformatics framework for False Discovery Rate (FDR)-controlled metabolite annotation for high-mass-resolution imaging mass spectrometry (https://github.com/alexandrovteam/pySM) introducing a Metabolite-Signal Match (MSM) score and a target-decoy FDR-estimate for spatial metabolomics. MALDI-FTICR datasets acquired from wild type adult mouse brain were used for the development of spatial metabolomics annotation bioinformatics. This study together with MTBLS317 and MTBLS378 provide the accompanying data for FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry.
2017-04-10 | MTBLS313 | MetaboLights
Project description:Autosomal recessive polycystic kidney disease is a severe, monogenetically inherited kidney and liver disease and PCK rats carrying the orthologous mutant gene serve as a model of human disease. We combined selective MALDI imaging of sulfated kidney lipids and Fisher discriminant analysis of imaging data sets for identification of candidate lipid markers of progressive disease in PCK rats. Our study highlights strong increases in lower mass lipids as main classifiers of cystic disease. Structure determination by high resolution mass spectrometry identifies these altered lipids as taurine-conjugated bile acids. Beside increased levels of serum-cholesterol these sulfated lipids are selectively elevated in the PCK rat model but not in models of related hepatorenal fibrocystic diseases suggesting that they be molecular markers of the disease. Genome-scale gene expression profiling of PCK and SD livers as control was performed to attempt elucidation of some of the underlying mechanisms leading to increases of cholesterol and taurine-conjugated bile acids in the PCK rat. Several pathways were found to be changed in cystic livers with up regulation or down regulation of important gene sets. Enhanced expression of steroid biosynthesis genes might result in the observed increased levels of cholesterol. In contrast, primary bile acid biosynthesis was found to be down regulated in diseased livers. These findings might be explained by compensatory mechanisms of liver metabolism to reduce toxic levels of accumulated bile acids. Snap-frozen liver tissue of 10 week old rats were subjected for RNA extraction and hybridization on Affymetrix microarrays to perform genome-scale gene expression profiling of n = 6 diseased PCK and n = 6 Sprague Dawley rat livers as control.
2013-12-01 | E-GEOD-48357 | biostudies-arrayexpress
Project description:Highly specialized cells are fundamental for proper functioning of complex organs. Variations in cell-type specific gene expression and protein composition have been linked to a variety of diseases. Although single cell technologies have emerged as valuable tools to address this cellular heterogeneity, a majority of these workflows lack sufficient in situ resolution for functional classification of cells and are associated with extremely long analysis time, especially when it comes to in situ proteomics. In addition, lack of understanding of single cell dynamics within their native environment limits our ability to explore the altered physiology in disease development. This limitation is particularly relevant in the mammalian brain, where different cell types perform unique functions and exhibit varying sensitivities to insults. The hippocampus, a brain region crucial for learning and memory, is of particular interest due to its obvious involvement in various neurological disorders. Here, we present a combination of experimental and data integration approaches for investigation of cellular heterogeneity and functional disposition within the mouse brain hippocampus using MALDI Imaging mass spectrometry (MALDI-IMS) and shotgun proteomics (LC-MS/MS) coupled with laser-capture microdissection (LCM) along with spatial transcriptomics. Within the dentate gyrus granule cells we identified two proteomically distinct cellular subpopulations that are characterized by a substantial number of discriminative proteins. These cellular clusters contribute to the overall functionality of the dentate gyrus by regulating redox homeostasis, mitochondrial organization, RNA processing, and microtubule organization. Importantly, most of the identified proteins matched their transcripts, verifying the in situ protein identification and supporting their functional analyses. By combining high-throughput spatial proteomics with transcriptomics, our approach enables reliable near-single-cell scale identification of proteins and profiling of inter-cellular heterogeneity within similar cell-types in tissues. This methodology has the potential to be applied to different biological conditions and tissues, providing a deeper understanding of cellular subpopulations in situ.
2024-07-24 | GSE242688 | GEO