Browse
Submit Data
Databases
API
Help

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Potential of Single Pulse and Multiplexed Drift-Tube Ion Mobility Spectrometry Coupled to Micropillar Array Column for Proteomics Studies.

ABSTRACT: Proteomics is one of the most significant methodologies to better understand the molecular pathways involved in diseases and to improve their diagnosis, treatment and follow-up. The investigation of the proteome of complex organisms is challenging from an analytical point of view, because of the large number of proteins present in a wide range of concentrations. In this study, nanofluidic chromatography, using a micropillar array column, was coupled to drift-tube ion mobility and time-of-flight mass spectrometry to identify as many proteins as possible in a protein digest standard of HeLa cells. Several chromatographic parameters were optimized. The high interest of drift-tube ion mobility to increase the number of identifications and to separate isobaric coeluting peptides was demonstrated. Multiplexed drift-tube ion mobility spectrometry was also investigated, to increase the sensitivity in proteomics studies. This innovative proteomics platform will be useful for analyzing patient samples to better understand unresolved disorders.

SUBMITTER: Nix C

PROVIDER: S-EPMC9319919 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Improved Sensitivity in Low-Input Proteomics Using Micropillar Array-Based Chromatography.

Project description:Capitalizing on the massive increase in sample concentrations which are produced by extremely low elution volumes, nanoliquid chromatography-electrospray ionization-tandem mass spectrometry (nano-LC-ESI-MS/MS) is currently one of the most sensitive analytical technologies for the comprehensive characterization of complex protein samples. However, despite tremendous technological improvements made in the production and the packing of monodisperse spherical particles for nanoflow high-pressure liquid chromatography (HPLC), current state-of-the-art systems still suffer from limits in operation at the maximum potential of the technology. With the recent introduction of the μPAC system, which provides perfectly ordered micropillar array based chromatographic support materials, completely new chromatographic concepts for optimization toward the needs of ultrasensitive proteomics become available. Here we report on a series of benchmarking experiments comparing the performance of a commercially available 50 cm micropillar array column to a widely used nanoflow HPLC column for the proteomics analysis of 10 ng of tryptic HeLa cell digest. Comparative analysis of LC-MS/MS-data corroborated that micropillar array cartridges provide outstanding chromatographic performance, excellent retention time stability, and increased sensitivity in the analysis of low-input proteomics samples and thus repeatedly yielded almost twice as many unique peptide and unique protein group identifications when compared to conventional nanoflow HPLC columns.

| S-EPMC6873107 | biostudies-literature

Ultra-Fast Polarity Switching, Non-Radioactive Drift Tube for the Miniaturization of Drift-Time Ion Mobility Spectrometer.

Project description:Drift-time ion mobility spectrometer (DT-IMS) is a promising technology for gas detection and analysis in the form of miniaturized instrument. Analytes may exist in the form of positively or negatively charged ions according to their chemical composition and ionization condition, and therefore require both polarity of electric field for the detection. In this work the polarity switching of a drift-time ion mobility spectrometer based on a direct current (DC) corona discharge ionization source was investigated, with novel solutions for both the control of ion shutter and the stabilization of aperture grid. The drift field is established by employing a switchable high voltage power supply and a serial of voltage regulator diode, with optocouplers to drive the ion shutter when the polarity is switched. The potential of aperture grid is stabilized during the polarity switching by the use of four diodes to avoid unnecessary charging cycle of the aperture grid capacitor. Based on the proposed techniques, the developed DT-IMS with 50 mm drift path is able to switch its polarity in 10 ms and acquire mobility spectrum after 10 ms of stabilization. Coupled with a thermal desorption sampler, limit of detection (LoD) of 0.1 ng was achieved for ketamine and TNT. Extra benefits include single calibration substance for both polarities and largely simplified pneumatic design, together with the reduction of second drift tube and its accessories. This work paved the way towards further miniaturization of DT-IMS without compromise of performance.

| S-EPMC9269308 | biostudies-literature

Flexible Drift Tube for High Resolution Ion Mobility Spectrometry (Flex-DT-IMS).

Project description:This paper describes, in detail, the development of a novel, low-cost, and flexible drift tube (DT) along with an associated ion mobility spectrometer system. The DT is constructed from a flexible printed circuit board (PCB), with a bespoke "dog-leg" track design, that can be rolled up for ease of assembly. This approach incorporates a shielding layer, as part of the flexible PCB design, and represents the minimum dimensional footprint conceivable for a DT. The low thermal mass of the polyimide substrate and overlapping electrodes, as afforded by the dog-leg design, allow for efficient heat management and high field linearity within the tube-achieved from a single PCB. This is further enhanced by a novel double-glazing configuration which provides a simple and effective means for gas management, minimizing thermal variation within the assembly. Herein, we provide a full experimental characterization of the flexible DT ion mobility spectrometer (Flex-DT-IMS) with corresponding electrodynamic (Simion 8.1) and fluid dynamic (SolidWorks) simulations. The Flex-DT-IMS is shown to have a resolution >80 and a detection limit of low nanograms for the analysis of common explosives (RDX, PETN, HMX, and TNT).

| S-EPMC7467419 | biostudies-literature

An Interlaboratory Evaluation of Drift Tube Ion Mobility-Mass Spectrometry Collision Cross Section Measurements.

Project description:Collision cross section (CCS) measurements resulting from ion mobility-mass spectrometry (IM-MS) experiments provide a promising orthogonal dimension of structural information in MS-based analytical separations. As with any molecular identifier, interlaboratory standardization must precede broad range integration into analytical workflows. In this study, we present a reference drift tube ion mobility mass spectrometer (DTIM-MS) where improvements on the measurement accuracy of experimental parameters influencing IM separations provide standardized drift tube, nitrogen CCS values (DTCCSN2) for over 120 unique ion species with the lowest measurement uncertainty to date. The reproducibility of these DTCCSN2 values are evaluated across three additional laboratories on a commercially available DTIM-MS instrument. The traditional stepped field CCS method performs with a relative standard deviation (RSD) of 0.29% for all ion species across the three additional laboratories. The calibrated single field CCS method, which is compatible with a wide range of chromatographic inlet systems, performs with an average, absolute bias of 0.54% to the standardized stepped field DTCCSN2 values on the reference system. The low RSD and biases observed in this interlaboratory study illustrate the potential of DTIM-MS for providing a molecular identifier for a broad range of discovery based analyses.

| S-EPMC5744684 | biostudies-literature

Differentiation of Polyamide 6, 6.6, and 12 Contaminations in Polyolefin-Recyclates Using HPLC Coupled to Drift-Tube Ion-Mobility Quadrupole Time-of-Flight Mass Spectrometry.

Project description:Recycling is a current hot topic with a focus especially on plastics. The quality of such plastic recyclates is of utmost importance for further processing because impurities lead to a reduction thereof. Contaminations originating from other polymers are highly problematic due to their immiscibility with the recyclate, leading to possible product failures. Therefore, methods for the determination of polymer impurities in recyclates should be investigated. In this paper, an approach for the identification of three different polyamide grades (polyamide 6, 6.6, and 12) is presented, applicable for the analysis of polyolefin-recyclates. An HPLC equipped with a drift-tube ion-mobility QTOF-MS was used for the identification and differentiation of compounds originating from the polyamides, which were then used as markers. These marker compounds are specific for each type and can be identified by their corresponding value of the collision cross section (CCS). After a simple sample preparation, all three types of polyamides were identified within one measurement. In particular, the problematic differentiation of polyamide 6 and 6.6 was easily made possible.

| S-EPMC8235147 | biostudies-literature

Electrochemical Performance of Micropillar Array Electrodes in Microflows.

Project description:The microchip-based electrochemical detection system (μEDS) has attracted plenty of research attention due to its merits including the capability in high-density integration, high sensitivity, fast analysis time, and reduced reagent consumption. The miniaturized working electrode is usually regarded as the core component of the μEDS, since its characteristic directly determines the performance of the whole system. Compared with the microelectrodes with conventional shapes such as the band, ring and disk, the three-dimensional (3D) micropillar array electrode (μAE) has demonstrated significant potential in improving the current response and decreasing the limits of detection due to its much larger reaction area. In this study, the numerical simulation method was used to investigate the performance of the μEDS, and both the geometrical and hydrodynamic parameters, including the micropillars shape, height, arrangement form and the flow rate of the reactant solution, were taken into consideration. The tail effect in μAEs was also quantitatively analyzed based on a pre-defined parameter of the current density ratio. In addition, a PDMS-based 3D μAE was fabricated and integrated into the microchannel for the electrochemical detection. The experiments of cyclic voltammetry (CV) and chronoamperometry (CA) were conducted, and a good agreement was found between the experimental and simulation results. This study would be instructive for the configuration and parameters design of the μEDS, and the presented method can be adopted to analyze and optimize the performance of nanochip-based electrochemical detection system (nEDS).

| S-EPMC7570346 | biostudies-literature

Collision-Induced Unfolding Studies of Proteins and Protein Complexes using Drift Tube Ion Mobility-Mass Spectrometer.

Project description:Elucidating the structures and stabilities of proteins and their complexes is paramount to understanding their biological functions in cellular processes. Native mass spectrometry (MS) coupled with ion mobility spectrometry (IMS) is emerging as an important biophysical technique owing to its high sensitivity, rapid analysis time, and ability to interrogate sample complexity or heterogeneity and the ability to probe protein structure dynamics. Here, a commercial IMS-MS platform has been modified for static native ESI emitters and an extended mass-to-charge range (20 kDa m/z) and its performance capabilities and limits were explored for a range of protein and protein complexes. The results show new potential for this instrument platform for studies of large protein and protein complexes and provides a roadmap for extending the performance metrics for studies of even larger, more complex systems, namely, membrane protein complexes and their interactions with ligands.

| S-EPMC7289629 | biostudies-literature

Bridged Hybrid Monolithic Column Coupled to High-Resolution Mass Spectrometry for Top-Down Proteomics.

Project description:Top-down mass spectrometry (MS)-based proteomics has become a powerful tool for comprehensive characterization of intact proteins. However, because of the high complexity of the proteome, highly effective separation of intact proteins from complex mixtures prior to MS analysis remains challenging. Monolithic columns have shown great promise for intact protein separation due to their high permeability, low backpressure, and fast mass transfer. Herein, for the first time, we developed bridged hybrid bis(triethoxysilyl)ethylene (BTSEY) monolith with C8 functional groups (C8@BTSEY) for highly effective protein separation and coupled it to high-resolution MS for identification of intact proteins from complex protein mixtures. We have optimized mobile phase conditions of our monolith-based reverse-phase chromatography (RPC) for online liquid chromatography (LC)-MS analysis and evaluated separation reproducibility of the C8@BTSEY column. We further assessed the chromatographic performance of this column by separating a complex protein mixture extracted from swine heart tissue. Using our monolithic column (i.d. 100 μm × 35 cm), we separated over 300 proteoforms (up to 104 kDa) from 360 ng of protein mixture in an 80 min one-dimensional (1D) LC run. The highly effective separation and recovery of intact proteins from this monolithic column allowed unambiguous identification of ∼100 proteoforms including a large protein, αactinin2 (103.77 kDa), by online 1D LC-MS/MS analysis for the first time. As demonstrated, this C8@BTSEY column is reproducible and effective in separation of intact proteins, which shows high promise for top-down proteomics.

| S-EPMC6491350 | biostudies-literature

Resolving structural isomers of monosaccharide methyl glycosides using drift tube and traveling wave ion mobility mass spectrometry.

Project description:Monosaccharide structural isomers including sixteen methyl-D-glycopyranosides and four methyl-N-acetylhexosamines were subjected to ion mobility measurements by electrospray ion mobility mass spectrometry. Two ion mobility-MS systems were employed: atmospheric pressure drift tube ion mobility time-of-flight mass spectrometry and a Synapt G2 HDMS system which incorporates a low pressure traveling wave ion mobility separator. All the compounds were investigated as [M + Na](+) ions in the positive mode. A majority of the monosaccharide structural isomers exhibited different mobility drift times in either system, depending on differences in their anomeric and stereochemical configurations. In general, drift time patterns (relative drift times of isomers) matched between the two instruments. Higher resolving power was observed using the atmospheric pressure drift tube. Collision cross section values of monosaccharide structural isomers were directly calculated from the atmospheric pressure ion mobility experiments, and a collision cross section calibration curve was made for the traveling wave ion mobility instrument. Overall, it was demonstrated that ion mobility-mass spectrometry using either drift tube or traveling wave ion mobility is a valuable technique for resolving subtle variations in stereochemistry among the sodium adducts of monosaccharide methyl glycosides.

| S-EPMC3633476 | biostudies-literature

Automated flow injection method for the high precision determination of drift tube ion mobility collision cross sections.

Project description:The field of ion mobility-based omics studies requires high-quality collision cross section (CCS) libraries to effectively utilize CCS as a molecular descriptor. Absolute CCS values with the highest precision are obtained on drift tube instruments by measuring the drift time of ions at multiple drift voltages, commonly referred to as a 'stepped field' experiment. However, generating large scale absolute CCS libraries from drift tube instruments is time consuming due to the current lack of high-throughput methods. This communication reports a fully automated stepped-field method to acquire absolute CCS on commercially available equipment. Using a drift tube ion mobility-mass spectrometer (DTIM-MS) coupled to a minimally modified liquid chromatography (LC) system, CCS values can be measured online with a carefully timed flow injection analysis (FIA) experiment. Results demonstrate that the FIA stepped-field method yields CCS values which are of high analytical precision (<0.4% relative standard deviation, RSD) and accuracy (?0.4% difference) comparable to CCS values obtained using traditional direct-infusion stepped-field experiments. This high-throughput CCS method consumes very little sample volume (20 ?L) and will expedite the generation of large-scale CCS libraries to support molecular identification within global untargeted studies.

| S-EPMC5869168 | 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