Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

An algorithm for correcting systematic energy deficits in the atom probe mass spectra of insulating samples.

ABSTRACT: Improvements in the mass resolution of a mass spectrometer directly correlate to improvements in peak identification and quantification. Here, we describe a post-processing technique developed to increase the quality of mass spectra of strongly insulating samples in laser-pulsed atom probe microscopy. The technique leverages the self-similarity of atom probe mass spectra collected at different times during an experimental run to correct for electrostatic artifacts that present as systematic energy deficits. We demonstrate the method on fused silica (SiO2) and neodymium-doped ceria (CeO2) samples which highlight the improvements that can be made to the mass spectrum of strongly insulating samples.

SUBMITTER: Caplins BW

PROVIDER: S-EPMC7536741 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

An algorithm for correcting systematic energy deficits in the atom probe mass spectra of insulating samples.

Caplins Benjamin W BW Blanchard Paul T PT Chiaramonti Ann N AN Diercks David R DR Miaja-Avila Luis L Sanford Norman A NA

Ultramicroscopy 20200415

Improvements in the mass resolution of a mass spectrometer directly correlate to improvements in peak identification and quantification. Here, we describe a post-processing technique developed to increase the quality of mass spectra of strongly insulating samples in laser-pulsed atom probe microscopy. The technique leverages the self-similarity of atom probe mass spectra collected at different times during an experimental run to correct for electrostatic artifacts that present as systematic ener ...[more]

PMID: 32408251

Similar Datasets

Fast-atom-bombardment mass spectra of enkephalins.

Project description:The positive- and negative-ion mass spectra of [methionine]enkephalin and [leucine]enkephalin have been obtained by using a fast-atom-bombardment source described previously by Barber, Bordoli, Sedgwick & Tyler [(1981) J. Chem. Soc. Chem. Commun., in the press]. This technique has allowed the spectra to be obtained without conversion of the enkephalins into volatile derivatives. The fast-atom-bombardment spectra show good pseudo-molecular-ion sensitivity and fragmentation that can be interpreted on the basis of the known molecular structure.

| S-EPMC1163139 | biostudies-other

Exploring the accuracy of isotopic analyses in atom probe mass spectrometry.

Project description:Atom probe tomography (APT) can theoretically deliver accurate chemical and isotopic analyses at a high level of sensitivity, precision, and spatial resolution. However, empirical APT data often contain significant biases that lead to erroneous chemical concentration and isotopic abundance measurements. The present study explores the accuracy of quantitative isotopic analyses performed via atom probe mass spectrometry. A machine learning-based adaptive peak fitting algorithm was developed to provide a reproducible and mathematically defensible means to determine peak shapes and intensities in the mass spectrum for specific ion species. The isotopic abundance measurements made with the atom probe are compared directly with the known isotopic abundance values for each of the materials. Even in the presence of exceedingly high numbers of multi-hit detection events (up to 80%), and in the absence of any deadtime corrections, our approach produced isotopic abundance measurements having an accuracy consistent with values limited predominantly by counting statistics.

| S-EPMC7717065 | biostudies-literature

A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.

Project description:The acquisition of high-resolution tandem mass spectra (MS/MS) is becoming more prevalent in proteomics, but most researchers employ peptide identification algorithms that were designed prior to this development. Here, we demonstrate new software, Morpheus, designed specifically for high-mass accuracy data, based on a simple score that is little more than the number of matching products. For a diverse collection of data sets from a variety of organisms (E. coli, yeast, human) acquired on a variety of instruments (quadrupole-time-of-flight, ion trap-orbitrap, and quadrupole-orbitrap) in different laboratories, Morpheus gives more spectrum, peptide, and protein identifications at a 1% false discovery rate (FDR) than Mascot, Open Mass Spectrometry Search Algorithm (OMSSA), and Sequest. Additionally, Morpheus is 1.5 to 4.6 times faster, depending on the data set, than the next fastest algorithm, OMSSA. Morpheus was developed in C# .NET and is available free and open source under a permissive license.

| S-EPMC3586292 | biostudies-literature

MS Amanda, a universal identification algorithm optimized for high accuracy tandem mass spectra.

Project description:Today's highly accurate spectra provided by modern tandem mass spectrometers offer considerable advantages for the analysis of proteomic samples of increased complexity. Among other factors, the quantity of reliably identified peptides is considerably influenced by the peptide identification algorithm. While most widely used search engines were developed when high-resolution mass spectrometry data were not readily available for fragment ion masses, we have designed a scoring algorithm particularly suitable for high mass accuracy. Our algorithm, MS Amanda, is generally applicable to HCD, ETD, and CID fragmentation type data. The algorithm confidently explains more spectra at the same false discovery rate than Mascot or SEQUEST on examined high mass accuracy data sets, with excellent overlap and identical peptide sequence identification for most spectra also explained by Mascot or SEQUEST. MS Amanda, available at http://ms.imp.ac.at/?goto=msamanda , is provided free of charge both as standalone version for integration into custom workflows and as a plugin for the Proteome Discoverer platform.

| S-EPMC4119474 | biostudies-literature

An Integrated Microfluidic Probe for Mass Spectrometry Imaging of Biological Samples*.

Project description:Ambient ionization based on liquid extraction is widely used in mass spectrometry imaging (MSI) of molecules in biological samples. The development of nanospray desorption electrospray ionization (nano-DESI) has enabled the robust imaging of tissue sections with high spatial resolution. However, the fabrication of the nano-DESI probe is challenging, which limits its dissemination to the broader scientific community. Herein, we describe the design and performance of an integrated microfluidic probe (iMFP) for nano-DESI MSI. The glass iMFP, fabricated using photolithography, wet etching, and polishing, shows comparable performance to the capillary-based nano-DESI MSI in terms of stability and sensitivity; a spatial resolution of better than 25 μm was obtained in these first proof-of-principle experiments. The iMFP is easy to operate and align in front of a mass spectrometer, which will facilitate broader use of liquid-extraction-based MSI in biological research, drug discovery, and clinical studies.

| S-EPMC8138756 | biostudies-literature

A single atom change turns insulating saturated wires into molecular conductors.

Project description:We present an efficient strategy to modulate tunnelling in molecular junctions by changing the tunnelling decay coefficient, β, by terminal-atom substitution which avoids altering the molecular backbone. By varying X = H, F, Cl, Br, I in junctions with S(CH2)(10-18)X, current densities (J) increase >4 orders of magnitude, creating molecular conductors via reduction of β from 0.75 to 0.25 Å-1. Impedance measurements show tripled dielectric constants (εr) with X = I, reduced HOMO-LUMO gaps and tunnelling-barrier heights, and 5-times reduced contact resistance. These effects alone cannot explain the large change in β. Density-functional theory shows highly localized, X-dependent potential drops at the S(CH2)nX//electrode interface that modifies the tunnelling barrier shape. Commonly-used tunnelling models neglect localized potential drops and changes in εr. Here, we demonstrate experimentally that [Formula: see text], suggesting highly-polarizable terminal-atoms act as charge traps and highlighting the need for new charge transport models that account for dielectric effects in molecular tunnelling junctions.

| S-EPMC8187423 | biostudies-literature

Quantifying biological samples using Linear Poisson Independent Component Analysis for MALDI-ToF mass spectra.

Project description:Motivation:Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI) facilitates the analysis of large organic molecules. However, the complexity of biological samples and MALDI data acquisition leads to high levels of variation, making reliable quantification of samples difficult. We present a new analysis approach that we believe is well-suited to the properties of MALDI mass spectra, based upon an Independent Component Analysis derived for Poisson sampled data. Simple analyses have been limited to studying small numbers of mass peaks, via peak ratios, which is known to be inefficient. Conventional PCA and ICA methods have also been applied, which extract correlations between any number of peaks, but we argue makes inappropriate assumptions regarding data noise, i.e. uniform and Gaussian. Results:We provide evidence that the Gaussian assumption is incorrect, motivating the need for our Poisson approach. The method is demonstrated by making proportion measurements from lipid-rich binary mixtures of lamb brain and liver, and also goat and cow milk. These allow our measurements and error predictions to be compared to ground truth. Availability and implementation:Software is available via the open source image analysis system TINA Vision, www.tina-vision.net. Contact:paul.tar@manchester.ac.uk. Supplementary information:Supplementary data are available at Bioinformatics online.

| S-EPMC5860625 | biostudies-literature

A hierarchical MS2/MS3 database search algorithm for automated analysis of phosphopeptide tandem mass spectra.

Project description:A novel hierarchical MS(2)/MS(3) database search algorithm has been developed to analyze MS(2)/MS(3) phosphopeptides proteomic data. The algorithm is incorporated in an automated database search program, MassMatrix. The algorithm matches experimental MS(2) spectra against a supplied protein database to determine candidate peptide matches. It then matches the corresponding experimental MS(3) spectra against those candidate peptide matches. The MS(2) and MS(3) spectra are used in concert to arrive at peptide matches with overall higher confidence rather than combining MS(2) and MS(3) data searched separately. Receiver operating characteristic analysis showed that hierarchical MS(2)/MS(3) database searches with MassMatrix had better sensitivity and specificity than the two-stage MS(2)/MS(3) database searches obtained with MassMatrix, MASCOT, and X!Tandem. A greater number of true peptide matches at a given false rate were identified by use of this new algorithm for data collected on both LCQ and LTQ-FTICR mass spectrometers. The additional MS(3) spectral data also improved the overall reliability and the number of true positives (TPs) due to the fact that the TPs of the MS(2)/MS(3) search results had higher scores than those of the MS(2).

| S-EPMC2775432 | biostudies-literature

GlycoDeNovo - an Efficient Algorithm for Accurate de novo Glycan Topology Reconstruction from Tandem Mass Spectra.

Project description:A major challenge in glycomics is the characterization of complex glycan structures that are essential for understanding their diverse roles in many biological processes. We present a novel efficient computational approach, named GlycoDeNovo, for accurate elucidation of the glycan topologies from their tandem mass spectra. Given a spectrum, GlycoDeNovo first builds an interpretation-graph specifying how to interpret each peak using preceding interpreted peaks. It then reconstructs the topologies of peaks that contribute to interpreting the precursor ion. We theoretically prove that GlycoDeNovo is highly efficient. A major innovative feature added to GlycoDeNovo is a data-driven IonClassifier which can be used to effectively rank candidate topologies. IonClassifier is automatically learned from experimental spectra of known glycans to distinguish B- and C-type ions from all other ion types. Our results showed that GlycoDeNovo is robust and accurate for topology reconstruction of glycans from their tandem mass spectra. Graphical Abstract ?.

| S-EPMC5647224 | biostudies-literature

Algorithm for correcting optimization convergence errors in Eclipse.

Project description:IMRT plans generated in Eclipse use a fast algorithm to evaluate dose for optimization and a more accurate algorithm for a final dose calculation, the Analytical Anisotropic Algorithm. The use of a fast optimization algorithm introduces optimization convergence errors into an IMRT plan. Eclipse has a feature where optimization may be performed on top of an existing base plan. This feature allows for the possibility of arriving at a recursive solution to optimization that relies on the accuracy of the final dose calculation algorithm and not the optimizer algorithm. When an IMRT plan is used as a base plan for a second optimization, the second optimization can compensate for heterogeneity and modulator errors in the original base plan. Plans with the same field arrangement as the initial base plan may be added together by adding the initial plan optimal fluence to the dose correcting plan optimal fluence.A simple procedure to correct for optimization errors is presented that may be implemented in the Eclipse treatment planning system, along with an Excel spreadsheet to add optimized fluence maps together.

| S-EPMC5720570 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data