Human cerebrospinal fluid analysis by data-independent analysis The Cerebrospinal fluid samples were denaturated and reduced.
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Brain
DISEASE(S): Parkinson's Disease
SUBMITTER: 
Lukas Schilde
LAB HEAD: Prof. Dr. Katrin Marcus
PROVIDER: PXD022234 | Pride | 2021-09-09
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 124_Peptides_CSF.xlsx | Xlsx | |||
| QEXI21308.raw.md5 | Raw | |||
| QEXI21308.raw.tar.gz | Raw | |||
| QEXI21308.raw.tar.gz.md5 | Raw | |||
| QEXI21310.raw.md5 | Raw |
Items per page: 5 1 - 5 of 373 |
Publications
MicroRNAs from extracellular vesicles as a signature for Parkinson's disease.
Caldi Gomes Lucas L Roser Anna-Elisa AE Jain Gaurav G Pena Centeno Tonatiuh T Maass Fabian F Schilde Lukas L May Caroline C Schneider Anja A Bähr Mathias M Marcus Katrin K Fischer André A Lingor Paul P
Clinical and translational medicine 20210401 4
Similar Datasets
Project description:Cerebrospinal fluid samples of patients with Parkinson’s disease and healthy controls were used for this study. Part of the samples consisted of fractions that were separated by gel electrophoresis. After tryptic digestion, all samples were spiked with indexed retention time (iRT) peptides and were measured using a DDA mass spectrometry approach. This data is intended to be used to create a spectral library for DIA analysis.
2020-08-13 | PXD013487 | Pride
Project description:Amino acids play key roles in the function of the central nervous system, and their alterations are implicated in psychiatric disorders. In the search for a biomarker for major depressive disorder (MDD), we used high-performance liquid chromatography to measure amino acids and related molecules in the cerebrospinal fluid (CSF) of 52 patients with MDD (42 depressed and 10 remitted; DSM-IV) and 54 matched controls. Significant differences were found in four amino acid concentrations between the depressed patients and controls. After Bonferroni correction, only ethanolamine (EA) levels remained significantly reduced in depressed patients (nominal P = 0.0000011). A substantial proportion of the depressed patients (40.5%) showed abnormally low CSF EA levels (<12.1 μM) (P = 0.000033; OR = 11.6, 95% CI: 3.1-43.2). When patients with low EA and those with high EA levels were compared, the former had higher scores for overall depression severity (P = 0.0033) and 'Somatic Anxiety' symptoms (P = 0.00026). In unmedicated subjects, CSF EA levels showed a significant positive correlation with levels of homovanillic acid (P = 0.0030) and 5-hydroxyindoleacetic acid (P = 0.019). To our knowledge, this is the first study showing that patients with MDD have significantly lower CSF EA concentrations compared with control subjects. CSF EA could be a state-dependent biomarker for a subtype of MDD.
| S-EPMC4295090 | biostudies-literature
Project description:Glioblastoma is a malignant brain tumor with mean overall survival of less than 15 months. Blood vessel leakage and peritumoral edema lead to increased intracranial pressure and augment neurological deficits which profoundly decrease the quality of life of glioblastoma patients. It is unknown how the dynamics of cerebrospinal fluid (CSF) turnover are affected during this process. By monitoring the transport of CSF tracers to the systemic blood circulation after infusion into the cisterna magna, we demonstrate that the outflow of CSF is dramatically reduced in glioma-bearing mice. Using a combination of magnetic resonance imaging (MRI) and near-infrared (NIR) imaging, we found that the circulation of CSF tracers was hindered after cisterna magna injection with reduced signals along the exiting cranial nerves and downstream lymph nodes, which represent the major CSF outflow route in mice. Due to blockage of the normal routes of CSF bulk flow within and from the cranial cavity, CSF tracers were redirected into the spinal space. In some mice, impaired CSF clearance from the cranium was compensated by a lymphatic outflow from the sacral spine.
| S-EPMC6794292 | biostudies-literature
Project description:This article provides a detailed dataset of human tear fluid proteins. Samples were fractionated by sodium dodecyl sulfate (SDS) gel electrophoresis resulting in 48 fractions that were spiked with an indexed retention time (iRT) peptide standard. These data are based on a data-dependent acquisition (DDA) mass spectrometric approach and can be used for example as a spectral library for tear fluid proteome analysis by data-independent acquisition (DIA). Moreover, the provided data set can be used with optimized HPLC as well as mass spectrometric settings for proteins/peptides of interest. Besides these aspects, this dataset can serve as a protein overview for gene ontology enrichment analysis as well as for modeling and benchmarking of multiple signaling pathways associated with the ocular surface in healthy or disease stages.
2019-08-15 | PXD011075 | Pride
Project description:A progressive loss of protein homeostasis is characteristic of aging and a driver of neurodegeneration. To investigate this process quantitatively, we characterized proteome dynamics during brain aging in the short-lived vertebrate Nothobranchius furzeri combining transcriptomics and proteomics. We detected a progressive reduction in the correlation between protein and mRNA mainly due to post-transcriptional mechanisms that account for over 40% of the age-regulated proteins. These changes cause a progressive loss of stoichiometry in several protein complexes, including ribosomes, which show impaired assembly and are enriched in protein aggregates in old brains. Mechanistically, we show that reduction of proteasome activity is an early event during brain aging and is sufficient to induce proteomic signatures of aging and loss of stoichiometry in vivo. Using longitudinal transcriptomic data, we show that the magnitude of early life decline in proteasome levels is the major risk factor for mortality. Our work defines causative events in the aging process that can be targeted to prevent loss of protein homeostasis and delay the onset of age-related neurodegeneration.
2020-06-22 | PXD016459 | Pride
Project description:BACKGROUND:The autotaxin/lysophosphatidic acid axis is involved in diverse biological processes including neurodevelopment, inflammation, and immunological functioning. The lysophosphatidic acid 1 receptor has been implicated in the pathophysiology of major depressive disorder and in the mechanism of action of antidepressants. However, it is unclear whether central or peripheral autotaxin levels are altered in patients with major depressive disorder. METHODS:Serum autotaxin levels were measured by an enzyme-linked immunosorbent assay in 37 patients with major depressive disorder diagnosed using DSM-IV-TR who underwent electroconvulsive therapy and were compared with those of 47 nondepressed controls matched for age and sex between January 2011 and December 2015. Patient serum levels of autotaxin before and after electroconvulsive therapy were also compared. In a separate sample set, cerebrospinal fluid autotaxin levels were compared between 26 patients with major depressive disorder and 27 nondepressed controls between December 2010 and December 2015. A potential association was examined between autotaxin levels and clinical symptoms assessed with the Hamilton Depression Rating Scale. RESULTS:Before electroconvulsive therapy, both serum and cerebrospinal fluidautotaxin levels were significantly lower in major depressive disorder patients than in controls (serum: P = .001, cerebrospinal fluid: P = .038). A significantly negative correlation between serum, but not cerebrospinal fluid, autotaxin levels and depressive symptoms was observed (P = .032). After electroconvulsive therapy, a parallel increase in serum autotaxin levels and depressive symptoms improvement was observed (P = .005). CONCLUSION:The current results suggest that serum autotaxin levels are reduced in a state-dependent manner. The reduction of cerebrospinal fluidautotaxin levels suggests a dysfunction in the autotaxin/lysophosphatidic acid axis in the brains of patients with major depressive disorder.
| S-EPMC6441130 | biostudies-literature
Project description:BackgroundContinuous circulation and drainage of cerebrospinal fluid (CSF) are essential for the elimination of CSF-borne metabolic products and neuronal function. While multiple CSF drainage pathways have been identified, the significance of each to normal drainage and whether there are differential changes at CSF outflow regions in the aging brain are unclear.MethodsDynamic in vivo imaging of near infrared fluorescently-labeled albumin was used to simultaneously visualize the flow of CSF at outflow regions on the dorsal side (transcranial and -spinal) of the central nervous system. This was followed by kinetic analysis, which included the elimination rate constants for these regions. In addition, tracer distribution in ex vivo tissues were assessed, including the nasal/cribriform region, dorsal and ventral surfaces of the brain, spinal cord, cranial dura, skull base, optic and trigeminal nerves and cervical lymph nodes.ResultsBased on the in vivo data, there was evidence of CSF elimination, as determined by the rate of clearance, from the nasal route across the cribriform plate and spinal subarachnoid space, but not from the dorsal dural regions. Using ex vivo tissue samples, the presence of tracer was confirmed in the cribriform area and olfactory regions, around pial blood vessels, spinal subarachnoid space, spinal cord and cervical lymph nodes but not for the dorsal dura, skull base or the other cranial nerves. Also, ex vivo tissues showed retention of tracer along brain fissures and regions associated with cisterns on the brain surfaces, but not in the brain parenchyma. Aging reduced CSF elimination across the cribriform plate but not that from the spinal SAS nor retention on the brain surfaces.ConclusionsCollectively, these data show that the main CSF outflow sites were the nasal region across the cribriform plate and from the spinal regions in mice. In young adult mice, the contribution of the nasal and cribriform route to outflow was much higher than from the spinal regions. In older mice, the contribution of the nasal route to CSF outflow was reduced significantly but not for the spinal routes. This kinetic approach may have significance in determining early changes in CSF drainage in neurological disorder, age-related cognitive decline and brain diseases.
| S-EPMC7706057 | biostudies-literature
Project description:The seed coat of black (iRT) soybean with the dominant R allele begins to accumulate cyanic pigments at the transition stage of seed development (300 – 400 mg fresh seed weight), whereas the brown (irT) nearly-isogenic seed coat with the recessive r allele lacks cyanic pigments at all stages of seed development. We used microarrays to determine global gene expression differences between black (iRT) and brown (irT) soybean seed coats at the transition stage of seed development (300 – 400 mg fresh seed weight). To identify the complete set of gene transcripts that are differentially expressed between the seed coats of black (iRT) and brown (irT) Clark isolines, seed coats were dissected at the transition stage of seed development (300 – 400 mg fresh seed weight) for microarray analysis using the Affymetrix Soybean GeneChip. To ensure seed coats were of the same stage of development, the days post anthesis, pod length, pod color, embryo morphology, and transcript levels of the developmental marker gene Gm-r1083-1191, a putative cutin biosynthesis gene, and DFR1 were ensured to be equivalent between black (iRT) and brown (irT) isolines.
2011-08-22 | E-GEOD-26208 | biostudies-arrayexpress
Project description:Targeted analysis of DIA data is a powerful mass spectrometric approach for comprehensive, reproducible and precise proteome quantitation. It requires a spectral library, which contains for all considered peptide precursor ions empirically determined fragment ion intensities and their predicted retention time. Retention times, however, are not comparable on an absolute scale, especially if heterogeneous measurements are combined. Here we present a method for high-precision prediction of retention time, which significantly improves the quality of targeted DIA analysis compared to in silico retention time prediction and the state of the art indexed retention time (iRT) normalization approach. We describe a high precision normalized retention time algorithm, which is implemented in the Spectronaut software. We furthermore investigate the influence of nine different experimental factors, such as chromatographic mobile and stationary phase, on iRT precision. In summary we show that using targeted analysis of DIA data with high precision iRT significantly increases sensitivity and data quality. The iRT values are generally transferable across a wide range of experimental conditions. Best results, however, are achieved if library generation and analytical measurements are performed on the same system.
2016-07-14 | PXD004188 | Pride