ABSTRACT: Human total plasma N-glycosylation as studied by MALDI-FTICR-MS, to obtain the association thereof with clinical markers of inflammation and metabolic health.
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.
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.
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.
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.
Project description:Absolute quantification of protein was performed by MALDI-LTQ using scramble internal standard (sIS) peptide. Mixtures of serial dilutions of fibrinogen peptides (final concentration: 50, 100, 250, 500 and 1000 fmol/μL), equal amounts of corresponding sIS peptides (final concentration: 500 fmol/μL) and serial dilutions of digested serum (final concentration: 0, 0.025, 0.05, 0.25 and 0.5 μg/μL) were analyzed by MALDI-MS/MS. We also analyzed immunoprecipitated (IP) α-fibrinogen in 0.05-5 μL of plasma by MALDI-MS/MS.
Project description:This study has investigated several parameters to obtain increased detection of the amyloid plaque intact protein profile, including a comparison of commonly used MALDI matrices, acid based reduction of signal suppression as well as the combination of strong acid based protein aggregate extraction from laser microdissection plaques to increase detection of proteoforms. Female APPPS1-21 transgenic mice were analyzed by MALDI Imaging with different matrices on a Ultraflextreme MALDI TOF/TOF instrument followed by data analysis in SCiLS Lab software. A combination of formic acid treatment of laser capture microdissected plaques was further utilized to expand the analysis and validation of amyloid plaques.
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.