Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Correlated matrix-assisted laser desorption/ionization mass spectrometry and fluorescent imaging of photocleavable peptide-coded random bead-arrays.

ABSTRACT:

Rationale

Rapidly performing global proteomic screens is an important goal in the post-genomic era. Correlated matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and fluorescent imaging of photocleavable peptide-coded random bead-arrays was evaluated as a critical step in a new method for proteomic screening that combines many of the advantages of MS with fluorescence-based microarrays.

Methods

Small peptide-coded model bead libraries containing up to 20 different bead species were constructed by attaching peptides to 30-34 µm diameter glass, agarose or TentaGel® beads using photocleavable biotin or a custom-designed photocleavable linker. The peptide-coded bead libraries were randomly arrayed into custom gold-coated micro-well plates with 45 µm diameter wells and subjected to fluorescence and MALDI mass spectrometric imaging (MALDI-MSI).

Results

Photocleavable mass-tags from individual beads in these libraries were spatially localized as ~65 µm spots using MALDI-MSI with high sensitivity and mass resolution. Fluorescently tagged beads were identified and correlated with their matching photocleavable mass-tags by comparing the fluorescence and MALDI-MS images of the same bead-array. Post-translational modification of the peptide Kemptide was also detected on individual beads in a photocleavable peptide-coded bead-array by MALDI-MSI alone, after exposure of the beads to protein kinase A (PKA).

Conclusions

Correlated MALDI-MS and fluorescent imaging of photocleavable peptide-coded random bead-arrays can provide a basis for performing global proteomic screening.

SUBMITTER: Lim MJ

PROVIDER: S-EPMC3894740 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Laser desorption ionization mass spectrometry on silicon nanowell arrays.

Project description:This paper describes a new technique for fabrication of nanostructured porous silicon (pSi) for laser desorption ionization mass spectrometry. Porous silicon nanowell arrays were prepared by argon plasma etching through an alumina mask. Porous silicon prepared in this way proved to be an excellent substrate for desorption/ionization on silicon (DIOS) mass spectrometry (MS) using adenosine, Pro-Leu-Gly tripeptide, and [Des-Arg(9)]-bradykinin as the model compounds. It also allows the analyses of complex biological samples such as a tryptic digest of bovine serum albumin and a carnitine standard mixture. Nanowell array surfaces were also used for direct quantification of the illicit drug fentanyl in red blood cell extracts. This method also allows full control of the surface features. MS results suggested that the pore depth has a significant effect on the ion signals. Significant improvement in the ionization was observed by increasing the pore depth from 10 to 50 nm. These substrates are useful for laser desorption ionization in both the atmospheric pressure and vacuum regimes.

| S-EPMC2939284 | biostudies-literature

macroMS: Image-Guided Analysis of Random Objects by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry.

Project description:Mass spectrometry imaging is well-suited to characterizing sample surfaces for their chemical content in a spatially resolved manner. However, when the surface contains small objects with significant empty spaces between them, more efficient approaches to sample acquisition are possible. Image-guided mass spectrometry (MS) enables high-throughput analysis of a diverse range of sample types, such as microbial colonies, liquid microdroplets, and others, by recognizing and analyzing selected location targets in an image. Here, we describe an imaging protocol and macroMS, an online software suite that can be used to enhance MS measurements of macroscopic samples that are imaged by a camera or a flatbed scanner. The web-based tool enables users to find and filter targets from the optical images, correct optical distortion issues for improved spatial location of selected targets, input the custom geometry files into an MS device to acquire spectra at the selected locations, and finally, perform limited data analysis and use visualization tools to aid locating samples containing compounds of interest. Using the macroMS suite, an enzyme mutant library of Saccharomyces cerevisiae and nL droplet arrays of Escherichia coli and Pseudomonas fluorescens have been assayed at a rate of ∼2 s/sample.

| S-EPMC8102432 | biostudies-literature

Mass Spectrometry Imaging of Lipids in Human Skin Disease Model Hidradenitis Suppurativa by Laser Desorption Ionization from Silicon Nanopost Arrays.

Project description:Neutral lipids have been implicated in a host of potentially debilitating human diseases, such as heart disease, type-2 diabetes, and metabolic syndrome. Matrix-assisted laser desorption ionization (MALDI), the method-of-choice for mass spectrometry imaging (MSI), has led to remarkable success in imaging several lipid classes from biological tissue sections. However, due to ion suppression by phospholipids, MALDI has limited ability to efficiently ionize and image neutral lipids, such as triglycerides (TGs). To help overcome this obstacle, we have utilized silicon nanopost arrays (NAPA), a matrix-free laser desorption ionization (LDI) platform. Hidradenitis suppurativa (HS) is a chronic, recurrent inflammatory skin disease of the apocrine sweat glands. The ability of NAPA to efficiently ionize lipids is exploited in the analysis of human skin samples from sufferers of HS. Ionization by LDI from NAPA allows for the detection and imaging of a number of neutral lipid species, including TGs comprised of shorter, odd-chain fatty acids, which strongly suggests an increased bacterial load within the host tissue, as well as hexosylceramides (HexCers) and galabiosyl-/lactosylceramides that appear to be correlated with the presence of HS. Our results demonstrate that NAPA-LDI-MSI is capable of imaging and potentially differentiating healthy and diseased human skin tissues based on changes in detected neutral lipid composition.

| S-EPMC6877612 | biostudies-literature

Profiling Protein Tyrosine Phosphatase Specificity with Self-Assembled Monolayers for Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry and Peptide Arrays.

Project description:The opposing activities of phosphatases and kinases determine the phosphorylation status of proteins, yet kinases have received disproportionate attention in studies of cellular processes, with the roles of phosphatases remaining less understood. This Research Article describes the use of phosphotyrosine-containing peptide arrays together with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to directly profile phosphatase substrate selectivities. Twenty-two protein tyrosine phosphatases were characterized with the arrays to give a profile of their specificities. An analysis of the data revealed that certain residues in the substrates had a conserved effect on activity for all enzymes tested, including the general rule that inclusion of a basic lysine or arginine residue on either side of the phosphotyrosine decreased activity. This insight also provides a new perspective on the role of a R1152Q mutant in the insulin receptor, which is known to exhibit a lower phosphorylation level and which this work suggests may be due to an increased activity toward phosphatase enzymes. The use of self-assembled monolayers for matrix-assisted laser desorption/ionization mass spectrometry (SAMDI-MS) to provide a rapid and quantitative assay of phosphatase enzymes will be important to gaining a more complete understanding of the biochemistry and biology of this important enzyme class.

| S-EPMC6848775 | biostudies-literature

Laser-induced acoustic desorption/atmospheric pressure chemical ionization mass spectrometry.

Project description:Laser-induced acoustic desorption (LIAD) was successfully coupled to a conventional atmospheric pressure chemical ionization (APCI) source in a commercial linear quadrupole ion trap mass spectrometer (LQIT). Model compounds representing a wide variety of different types, including basic nitrogen and oxygen compounds, aromatic and aliphatic compounds, as well as unsaturated and saturated hydrocarbons, were tested separately and as a mixture. These model compounds were successfully evaporated into the gas phase by using LIAD and then ionized by using APCI with different reagents. From the four APCI reagent systems tested, neat carbon disulfide provided the best results. The mixture of methanol and water produced primarily protonated molecules, as expected. However, only the most basic compounds yielded ions under these conditions. In sharp contrast, using APCI with either neat benzene or neat carbon disulfide as the reagent resulted in the ionization of all the analytes studied to predominantly yield stable molecular ions. Benzene yielded a larger fraction of protonated molecules than carbon disulfide, which is a disadvantage. A similar but minor amount of fragmentation was observed for these two reagents. When the experiment was performed without a liquid reagent (nitrogen gas was the reagent), more fragmentation was observed. Analysis of a known mixture as well as a petroleum cut was also carried out. In summary, the new experiment presented here allows the evaporation of thermally labile compounds, both polar and nonpolar, without dissociation or aggregation, and their ionization to predominantly form stable molecular ions.

| S-EPMC3073421 | biostudies-literature

Antireflection Surfaces for Biological Analysis Using Laser Desorption Ionization Mass Spectrometry.

Project description:Laser desorption ionization mass spectrometry (LDI-MS) is a primary tool for biological analysis. Its success relies on the use of chemical matrices that facilitate soft desorption and ionization of the biomolecules, which, however, also limits its application for metabolomics study due to the chemical interference by the matrix compounds. The requirement for sample pretreatment is also undesirable for direct sampling analysis or tissue imaging. In this study, antireflection (AR) metal surfaces were investigated as sample substrates for matrix-free LDI-MS. They were prepared through ultrafast laser processing, with high light-to-heat energy conversion efficiency. The morphology and micro/nanostructures on the metal surfaces could be adjusted and optimized by tuning the laser fabrication process. The super-high UV absorption at 97% enabled highly efficient thermal desorption and ionization of analytes. The analytical performance for the matrix-free LDI was explored by analyzing a variety of biological compounds, including carbohydrates, drugs, metabolites, and amino acids. Its applicability for direct analysis of complex biological samples was also demonstrated by direct analysis of metabolites in yeast cells.

| S-EPMC6750120 | biostudies-literature

Miniaturizing sample spots for matrix-assisted laser desorption/ionization mass spectrometry.

Project description:The trend of miniaturization in bioanalytical chemistry is shifting from technical development to practical application. In matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), progress in miniaturizing sample spots has been driven by the needs to increase sensitivity and speed, to interface with other analytical microtechnologies, and to develop miniaturized instrumentation.We review recent developments in miniaturizing sample spots for MALDI-MS. We cover both target modification and microdispensing technologies, and we emphasize the benefits with respect to sensitivity, throughput and automation.We hope that this review will encourage further method development and application of miniaturized sample spots for MALDI-MS, so as to expand applications in analytical chemistry, protein science and molecular biology.

| S-EPMC2744082 | biostudies-literature

Detection of Single Ag Nanoparticles Using Laser Desorption/Ionization Mass Spectrometry.

Project description:The detection of a single entity (molecule, cell, particle, etc.) was always a challenging subject. Here we demonstrate the detection of single Ag nanoparticles (NPs) using subatmospheric pressure laser desorption/ionization mass spectrometry (LDI MS). The sample preparation, measurement conditions, generated ions, and limiting experimental factors are discussed here. We detected from 84 to 95% of the deposited 80 nm Ag NPs. The presented LDI MS platform is an alternative to laser ablation inductively coupled plasma mass spectrometry for imaging distribution of individual NPs across the sample surface and has a great potential for multiplexed mapping of low-abundance biomarkers in tissues.

| S-EPMC10326916 | biostudies-literature

omniSpect: an open MATLAB-based tool for visualization and analysis of matrix-assisted laser desorption/ionization and desorption electrospray ionization mass spectrometry images.

Project description:We present omniSpect, an open source web- and MATLAB-based software tool for both desorption electrospray ionization (DESI) and matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging (MSI) that performs computationally intensive functions on a remote server. These functions include converting data from a variety of file formats into a common format easily manipulated in MATLAB, transforming time-series mass spectra into mass spectrometry images based on a probe spatial raster path, and multivariate analysis. OmniSpect provides an extensible suite of tools to meet the computational requirements needed for visualizing open and proprietary format MSI data.

| S-EPMC4983445 | biostudies-literature

Multiplexed imaging of nanoparticles in tissues using laser desorption/ionization mass spectrometry.

Project description:Imaging of nanomaterials in biological tissues provides vital information for the development of nanotherapeutics and diagnostics. Multiplexed imaging of different nanoparticles (NPs) greatly reduces costs, the need to use multiple animals, and increases the biodistribution information that can enhance diagnostic applications and accelerate the screening of potential therapeutics. Various approaches have been developed for imaging NPs; however, the readout of existing imaging techniques relies on specific properties of the core material or surface ligands, and these techniques are limited because of the relatively small number of NPs that can be simultaneously measured in a single experiment. Here, we demonstrate the use of laser desorption/ionization mass spectrometry (LDI-MS) in an imaging format to investigate surface chemistry dictated intraorgan distribution of NPs. This new LDI-MS imaging method enables multiplexed imaging of NPs with potentially unlimited readouts and without additional labeling of the NPs. It provides the capability to detect and image attomole levels of NPs with almost no interferences from biomolecules. Using this new imaging approach, we find that the intraorgan distributions of same-sized NPs are directly linked to their surface chemistry.

| S-EPMC3801209 | 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