Browse
Submit Data
Databases
API
Help

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complementing the pulp proteome via sampling with a picosecond infrared laser (PIRL).

ABSTRACT:

Objectives

The aim of this investigation was the detailed analysis of the human pulp proteome using the new picosecond infrared laser (PIRL)-based sampling technique, which is based on a completely different mechanism compared to mechanical sampling. Proteome analysis of healthy pulp can provide data to define changes in the proteome associated with dental disease.

Material and methods

Immediately after extraction of the entire, undamaged tooth, 15 wisdom teeth were deep frozen in liquid nitrogen and preserved at -80°C. Teeth were crushed, and the excised frozen pulps were conditioned for further analysis. The pulps were sampled using PIRL, and the aspirates digested with trypsin and analyzed with mass spectrometry. Pulp proteins were categorized according to their gene ontology terminus. Proteins identified exclusively in this study were searched in the Human Protein Atlas (HPA) for gaining information about the main known localization and function.

Results

A total of 1348 proteins were identified in this study. The comparison with prior studies showed a match of 72%. Twenty-eight percent of the proteins were identified exclusively in this study. Considering HPA, almost half of these proteins were assigned to tissues that could be pulp specific.

Conclusion

PIRL is releasing proteins from the dental pulp which are not dissolved by conventional sampling techniques. Clinical Relevance The presented data extend current knowledge on dental pulp proteomics in healthy teeth and can serve as a reference for studies on pulp proteomics in dental disease.

SUBMITTER: Feridouni Khamaneh Y

PROVIDER: S-EPMC8602158 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Rapid determination of medulloblastoma subgroup affiliation with mass spectrometry using a handheld picosecond infrared laser desorption probe.

Project description:Medulloblastoma (MB), the most prevalent malignant childhood brain tumour, consists of at least 4 distinct subgroups each of which possesses a unique survival rate and response to treatment. To rapidly determine MB subgroup affiliation in a manner that would be actionable during surgery, we subjected murine xenograft tumours of two MB subgroups (SHH and Group 3) to Mass Spectrometry (MS) profiling using a handheld Picosecond InfraRed Laser (PIRL) desorption probe and interface developed by our group. This platform provides real time MS profiles of tissue based on laser desorbed lipids and small molecules with only 5-10 seconds of sampling. PIRL-MS analysis of ex vivo MB tumours offered a 98% success rate in subgroup determination, observed over 194 PIRL-MS datasets collected from 19 independent tumours (∼10 repetitions each) utilizing 6 different established MB cell lines. Robustness was verified by a 5%-leave-out-and-remodel test. PIRL ablated tissue material was collected on a filter paper and subjected to high resolution LC-MS to provide ion identity assignments for the m/z values that contribute most to the statistical discrimination between SHH and Group 3 MB. Based on this analysis, rapid classification of MB with PIRL-MS utilizes a variety of fatty acid chains, glycerophosphates, glycerophosphoglycerols and glycerophosphocholines rapidly extracted from the tumours. In this work, we provide evidence that 5-10 seconds of sampling from ex vivo MB tissue with PIRL-MS can allow robust tumour subgroup classification, and have identified several biomarker ions responsible for the statistical discrimination of MB Group 3 and the SHH subgroup. The existing PIRL-MS platform used herein offers capabilities for future in vivo use.

| S-EPMC5628578 | biostudies-literature

Homogenization of tissues via picosecond-infrared laser (PIRL) ablation: Giving a closer view on the in-vivo composition of protein species as compared to mechanical homogenization.

Project description:Posttranslational modifications and proteolytic processing regulate almost all physiological processes. Dysregulation can potentially result in pathologic protein species causing diseases. Thus, tissue species proteomes of diseased individuals provide diagnostic information. Since the composition of tissue proteomes can rapidly change during tissue homogenization by the action of enzymes released from their compartments, disease specific protein species patterns can vanish. Recently, we described a novel, ultrafast and soft method for cold vaporization of tissue via desorption by impulsive vibrational excitation (DIVE) using a picosecond-infrared-laser (PIRL). Given that DIVE extraction may provide improved access to the original composition of protein species in tissues, we compared the proteome composition of tissue protein homogenates after DIVE homogenization with conventional homogenizations. A higher number of intact protein species was observed in DIVE homogenates. Due to the ultrafast transfer of proteins from tissues via gas phase into frozen condensates of the aerosols, intact protein species were exposed to a lesser extent to enzymatic degradation reactions compared with conventional protein extraction. In addition, total yield of the number of proteins is higher in DIVE homogenates, because they are very homogenous and contain almost no insoluble particles, allowing direct analysis with subsequent analytical methods without the necessity of centrifugation.Enzymatic protein modifications during tissue homogenization are responsible for changes of the in-vivo protein species composition. Cold vaporization of tissues by PIRL-DIVE is comparable with taking a snapshot at the time of the laser irradiation of the dynamic changes that occur continuously under in-vivo conditions. At that time point all biomolecules are transferred into an aerosol, which is immediately frozen.

| S-EPMC4767054 | biostudies-literature

Sampling and homogenization of nanoliter tissue with a nanosecond infrared laser (NIRL) for mass spectrometric proteomics

Project description:It was recently shown that ultrashort pulse infrared (IR) lasers, operating at the wavelength of the OH vibration stretching band of water, are highly efficient at softly sampling and homogenizing biological tissue. We utilized a nanosecond infrared laser (NIRL) for tissue sampling and homogenization with subsequent LC-MS/MS analysis for mass spectrometric proteomics. Sampling was performed with murine spleen and colon tissue with an ablation volume of 1.1 x 1.1 x0.4 mm³ (approx. 0.5 µl), determined with optical coherence tomography (OCT). The identified proteins of both tissues contained tissue type specific proteins correlating with the corresponding lists of the Human Protein Atlas. The results demonstrate that tissue sampling and homogenization of small tissue volumes less than 1 µL for subsequent mass spectrometric proteomics is feasible with a NIRL and therefore is an alternative towards sampling of tissue sections with laser capture microdissection (LCM).

2022-02-17 | PXD027700 | Pride

Homogenization of tissues via picosecond-infrared laser (PIRL) ablation: Giving a closer view on the in-vivo composition of protein species as compared to mechanical homogenization

Project description:Tissue samples from human tonsils and rat pancreas were subjected to a novel laser-based homogenization method, the PIRL-DIVE homogenization, and to a conventional mechanical tissue homogenization procedure (bead mill and a cryo-grinder). The protein species composition of the protein extracts were compared by differential proteome analysis using two-dimensional gel electrophoresis followed by LC-MS/MS analysis and one-dimensional gel electrophoresis (SDS-PAGE) followed by quantitative LC-MS/MS analysis.

2016-01-25 | PXD003434 | Pride

Layered Seed-Growth of AgGe Football-like Microspheres via Precursor-Free Picosecond Laser Synthesis in Water.

Project description:Hybrid particles are of great significance in terms of their adjustable optical, electronic, magnetic, thermal and mechanical properties. As a novel technique, laser ablation in liquids (LAL) is famous for its precursor-free, "clean" synthesis of hybrid particles with various materials. Till now, almost all the LAL-generated particles originate from the nucleation-growth mechanism. Seed-growth of particles similar to chemical methods seems difficult to be achieved by LAL. Here, we not only present novel patch-joint football-like AgGe microspheres with a diameter in the range of 1?~?7??m achievable by laser ablation in distilled water but also find direct evidences of their layered seed growth mechanism. Many critical factors contribute to the formation of AgGe microspheres: fast laser-generated plasma process provide an excellent condition for generating large amount of Ge and Ag ions/atoms, their initial nucleation and galvanic replacement reaction, while cavitation bubble confinement plays an important role for the increase of AgGe nuclei and subsequent layered growth in water after bubble collapse. Driven by work function difference, Ge acts as nucleation agent for silver during alloy formation. This new seed-growth mechanism for LAL technique opens new opportunities to develop a large variety of novel hybrid materials with controllable properties.

| S-EPMC4558578 | biostudies-literature

Picosecond Pulsed Laser Deposition of Metals and Metal Oxides.

Project description:In this work, we present the fabrication of thin films/nanostructures of metals and metal oxides using picosecond laser ablation. Two sets of experiments were performed: the depositions were carried out in vacuum and in air at atmospheric pressure. The subjects of investigation were the noble metals Au and Pt and the metal oxides ZnO and TiO2. We studied and compared the phase composition, microstructure, morphology, and physicochemical state of the as-deposited samples' surfaces in vacuum and in air. It was found that picosecond laser ablation performed in vacuum led to the fabrication of thin films with embedded and differently sized nanoparticles. The implementation of the same process in air at atmospheric pressure resulted in the fabrication of porous nanostructures composed of nanoparticles. The ablation of pure Pt metal in air led to the production of nanoparticles with an oxide shell. In addition, more defects were formed on the metal oxide surface when the samples were deposited in vacuum. Furthermore, the laser ablation process of pure Au metal in a picosecond regime in vacuum and in air was theoretically investigated using molecular dynamics simulation.

| S-EPMC10573754 | biostudies-literature

The Human Melanoma Proteome Atlas-Complementing the melanoma transcriptome.

Project description:The MM500 meta-study aims to establish a knowledge basis of the tumor proteome to serve as a complement to genome and transcriptome studies. Somatic mutations and their effect on the transcriptome have been extensively characterized in melanoma. However, the effects of these genetic changes on the proteomic landscape and the impact on cellular processes in melanoma remain poorly understood. In this study, the quantitative mass-spectrometry-based proteomic analysis is interfaced with pathological tumor characterization, and associated with clinical data. The melanoma proteome landscape, obtained by the analysis of 505 well-annotated melanoma tumor samples, is defined based on almost 16 000 proteins, including mutated proteoforms of driver genes. More than 50 million MS/MS spectra were analyzed, resulting in approximately 13,6 million peptide spectrum matches (PSMs). Altogether 13 176 protein-coding genes, represented by 366 172 peptides, in addition to 52 000 phosphorylation sites, and 4 400 acetylation sites were successfully annotated. This data covers 65% and 74% of the predicted and identified human proteome, respectively. A high degree of correlation (Pearson, up to 0.54) with the melanoma transcriptome of the TCGA repository, with an overlap of 12 751 gene products, was found. Mapping of the expressed proteins with quantitation, spatiotemporal localization, mutations, splice isoforms, and PTM variants was proven not to be predicted by genome sequencing alone. The melanoma tumor molecular map was complemented by analysis of blood protein expression, including data on proteins regulated after immunotherapy. By adding these key proteomic pillars, the MM500 study expands the knowledge on melanoma disease.

| S-EPMC8299047 | biostudies-literature

Tunable Picosecond Laser Pulses via the Contrast of Two Reverse Saturable Absorption Phases in a Waveguide Platform.

Project description:How to enhance the optical nonlinearity of saturable absorption materials is an important question to improve the functionality of various applications ranging from the high power laser to photonic computational devices. We demonstrate the saturable absorption (SA) of VO2 film attributed to the large difference of optical nonlinearities between the two states of the phase-transition materials (VO2). Such VO2 film demonstrated significantly improved performance with saturation intensity higher than other existing ultrathin saturable absorbers by 3 orders due to its unique nonlinear optical mechanisms in the ultrafast phase change process. Owing to this feature, a Q-switched pulsed laser was fabricated in a waveguide platform, which is the first time to achieve picosecond pulse duration and maintain high peak power. Furthermore, the emission of this VO2 waveguide laser can be flexibly switched between the continuous-wave (CW) and pulsed operation regimes by tuning the temperature of the VO2 film, which enables VO2-based miniature laser devices with unique and versatile functions.

| S-EPMC5181842 | biostudies-literature

Picosecond metrology of laser-driven proton bursts.

Project description:Tracking primary radiation-induced processes in matter requires ultrafast sources and high precision timing. While compact laser-driven ion accelerators are seeding the development of novel high instantaneous flux applications, combining the ultrashort ion and laser pulse durations with their inherent synchronicity to trace the real-time evolution of initial damage events has yet to be realized. Here we report on the absolute measurement of proton bursts as short as 3.5±0.7 ps from laser solid target interactions for this purpose. Our results verify that laser-driven ion acceleration can deliver interaction times over a factor of hundred shorter than those of state-of-the-art accelerators optimized for high instantaneous flux. Furthermore, these observations draw ion interaction physics into the field of ultrafast science, opening the opportunity for quantitative comparison with both numerical modelling and the adjacent fields of ultrafast electron and photon interactions in matter.

| S-EPMC4749984 | biostudies-other

Lipidome Analysis of Oropharyngeal Tumor Tissues Using Nanosecond Infrared Laser (NIRL) Tissue Sampling and Subsequent Mass Spectrometry.

Project description:Ultrashort pulse infrared lasers can simultaneously sample and homogenize biological tissue using desorption by impulsive vibrational excitation (DIVE). With growing attention on alterations in lipid metabolism in malignant disease, mass spectrometry (MS)-based lipidomic analysis has become an emerging topic in cancer research. In this pilot study, we investigated the feasibility of tissue sampling with a nanosecond infrared laser (NIRL) for the subsequent lipidomic analysis of oropharyngeal tissues, and its potential to discriminate oropharyngeal squamous cell carcinoma (OPSCC) from non-tumorous oropharyngeal tissue. Eleven fresh frozen oropharyngeal tissue samples were ablated. The produced aerosols were collected by a glass fiber filter, and the lipidomes were analyzed with mass spectrometry. Data was evaluated by principal component analysis and Welch's t-tests. Lipid profiles comprised 13 lipid classes and up to 755 lipid species. We found significant inter- and intrapatient alterations in lipid profiles for tumor and non-tumor samples (p-value < 0.05, two-fold difference). Thus, NIRL tissue sampling with consecutive MS lipidomic analysis is a feasible and promising approach for the differentiation of OPSCC and non-tumorous oropharyngeal tissue and may provide new insights into lipid composition alterations in OPSCC.

| S-EPMC10178251 | 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