GNPS - Positive and negative ionization mode LC-MS/MS of Mexican microbial mats
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ Orbitrap
ORGANISM(S): Environmental Samples <bacillariophyta> (ncbitaxon:33858)
SUBMITTER: 
Mario Figueroa
PROVIDER: MSV000092042 | GNPS | Fri May 26 12:33:00 BST 2023
REPOSITORIES: GNPS
Similar Datasets
Project description:Dichloromethane (DCM) extracts of aerial parts and roots of Waltheria indica analyzed in UHPLC-MS/MS in positive ionization mode. .raw, .mzML and MzMine2 processed files(spectra .mgf and feature table .csv) are available.
References:
Cretton, Sylvian, Stéphane Dorsaz, Antonio Azzollini, Quentin Favre-Godal, Laurence Marcourt, Samad Nejad Ebrahimi, Francine Voinesco, et al. 2016. “Antifungal Quinoline Alkaloids from Waltheria Indica.” Journal of Natural Products 79 (2): 300–307.
Cretton, S., L. Breant, L. Pourrez, C. Ambuehl, L. Marcourt, S. N. Ebrahimi, M. Hamburger, et al. 2014. “Antitrypanosomal Quinoline Alkaloids from the Roots of Waltheria Indica.” Journal of Natural Products 77 (10): 2304–11.
2021-12-06 | MSV000088521 | MassIVE
Project description:Drosophila melanogaster Ms, Myosuppressin, is expressed in 3 baseline experiment(s);
| FBgn0011581 | ExpressionAtlas
Project description:Drosophila melanogaster Ms, Myosuppressin, is differentially expressed in 11 experiment(s);
| FBgn0011581 | ExpressionAtlas
Project description:Glomus sp. MS strain:MS Genome sequencing
| PRJNA210520 | ENA
Project description:Methanosarcina barkeri MS strain:MS Raw sequence reads
| PRJNA613292 | ENA
Project description:Electrospray ionization (ESI) is often affected by corona discharge when spraying 100% aqueous solutions as the voltage that induces discharge can be well below the onset voltage of ESI. As a result, it is especially challenging to perform native mass spectrometry in negative ion mode where 100% aqueous solution is preferred. Here we report a simple instrumentation method to improve the performance of ESI in negative ion mode based on capillary vibrating sharp-edge spray ionization. By attaching a fused silica capillary emitter to a vibrating glass slide, improved signal quality is achieved for various analytes in aqueous solutions over applying ESI alone. Compared to commercial ESI sources using nebulization gas to reduce discharge, 10-100-fold enhancement in signal intensity and 3-10-fold improvement in S/N are achieved for various kinds of molecules including DNA, peptides, proteins, and oligosaccharides. Finally, the new method demonstrates utility for native mass spectrometry analysis of proteins and G-quadruplex DNA. The present method is expected to have great potential to be adopted by the scientific community because of its improved analytical performance, simplicity, and low cost.
| S-EPMC7318871 | biostudies-literature
Project description:Extracellular vesicles (EVs) are released by most cell types and are implicated in several biological and pathological processes, including multiple sclerosis (MS). In this study we performed RNA sequencing to analyze the diversity of microorganisms by assignment of reads using different taxa profilers. To diminish the risk of false positive biases derived from sample handling, we performed a similar analysis on EVs derived from known cultured bacterial species, as well as artificially-generated samples. Overall, we detect a range of microbial species in MS and healthy control (HC) samples, that are not detected in control samples, as well as species with differential abundance between MS and HC samples. These results reveal the relevance of putative communication of microbial species using EVs as a communication vector.
2024-05-07 | GSE255317 | GEO
Project description:Desorption electrospray ionization-mass spectrometry (DESI-MS) imaging was used to analyze unmodified human brain tissue sections from 39 subjects sequentially in the positive and negative ionization modes. Acquisition of both MS polarities allowed more complete analysis of the human brain tumor lipidome as some phospholipids ionize preferentially in the positive and others in the negative ion mode. Normal brain parenchyma, comprised of grey matter and white matter, was differentiated from glioma using positive and negative ion mode DESI-MS lipid profiles with the aid of principal component analysis along with linear discriminant analysis. Principal component-linear discriminant analyses of the positive mode lipid profiles was able to distinguish grey matter, white matter, and glioma with an average sensitivity of 93.2% and specificity of 96.6%, while the negative mode lipid profiles had an average sensitivity of 94.1% and specificity of 97.4%. The positive and negative mode lipid profiles provided complementary information. Principal component-linear discriminant analysis of the combined positive and negative mode lipid profiles, via data fusion, resulted in approximately the same average sensitivity (94.7%) and specificity (97.6%) of the positive and negative modes when used individually. However, they complemented each other by improving the sensitivity and specificity of all classes (grey matter, white matter, and glioma) beyond 90% when used in combination. Further principal component analysis using the fused data resulted in the subgrouping of glioma into two groups associated with grey and white matter, respectively, a separation not apparent in the principal component analysis scores plots of the separate positive and negative mode data. The interrelationship of tumor cell percentage and the lipid profiles is discussed, and how such a measure could be used to measure residual tumor at surgical margins.
| S-EPMC5033406 | biostudies-literature
Project description:Native mass spectrometry (nMS) provides insights into the structures and dynamics of biomacromolecules in their native-like states by preserving noncovalent interactions through "soft" electrospray ionization (ESI). For native proteins, the number of charges that are acquired scales with the surface area and mass. Here, we explore the effect of highly negatively charged DNA on the ESI charge of protein complexes and find a reduction of the mass-to-charge ratio as well as a greater variation. The charge state distributions of pure DNA assemblies show a lower mass-to-charge ratio than proteins due to their greater density in the gas phase, whereas the charge of protein-DNA complexes can additionally be influenced by the distribution of the ESI charges, ion pairing events, and collapse of the DNA components. Our findings suggest that structural features of protein-DNA complexes can result in lower charge states than expected for proteins.
| S-EPMC11622369 | biostudies-literature
Project description:Negative ion mode nanoelectrospray ionization (nESI) is often utilized to analyze acidic compounds, from small molecules to proteins, with mass spectrometry (MS). Under high aqueous solvent conditions, corona discharge is commonly observed at emitter tips, resulting in low ion abundances and reduced nESI needle lifetimes. We have successfully reduced corona discharge in negative ion mode by trace addition of trifluoroethanol (TFE) to aqueous samples. The addition of as little as 0.2% TFE increases aqueous spray stability not only in nESI direct infusion, but also in nanoflow liquid chromatography (nLC)/MS experiments. Negative ion mode spray stability with 0.2% TFE is approximately 6× higher than for strictly aqueous samples. Upon addition of 0.2% TFE to the mobile phase of nLC/MS experiments, tryptic peptide identifications increased from 93 to 111 peptides, resulting in an average protein sequence coverage increase of 18%.
| S-EPMC5642034 | biostudies-literature