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Spectrometry

Spectrometry is a powerful analytical technique that enables the identification and quantification of chemical compounds by measuring the interaction between matter and electromagnetic radiation.
This non-destructive method can be applied to a wide range of samples, from biological macromolecules to complex industrial mixtures.
Spectrometric techniques involve the separation of light into its constituent wavelengths, followed by the detection and analysis of the resulting spectrum.
These measurements provide valuable information about the chemical composition, structure, and properties of the analyte.
Spectrometry plays a crucial role in fields such as chemistry, physics, biology, and environmental science, facilitating advanced research, quality control, and diagnostic applications.
With continual advancements in instrumentation and data analysis, spectrometry remains an indispensable tool for scientists seeking to unveil the secrets of the physical world.

Most cited protocols related to «Spectrometry»

We performed a laboratory analysis to construct an experimental dataset of proteins from a Gram-negative bacterium, Pseudomonas aeruginosa PA01, which was used to assess PSORTb 2.0, PSORTb 3.0, PA 2.5 and PA 3.0. This represents an independent dataset that includes hypothetical and uncharacterized proteins with previously unknown SCLs. P.aeruginosa is a bacterium noted for its diverse metabolic capacity and large genome/proteome size, and so represents an excellent organism with which to generate such a dataset (Stover et al., 2000 (link)). To generate this experimental dataset, we extracted protein samples from the cytoplasmic, periplasmic and secreted fractions of P.aeruginosa PA01. The resulting proteins in each fraction were digested to peptides and differentially labeled using formaldehyde isotopologues (Chan and Foster, 2008 (link)) prior to analysis by liquid chromatography–tandem mass spectrometry (LC–MS/MS), exactly as previously described (Chan et al., 2006 (link)). Abundance ratios between SCL were calculated using MSQuant (http://msquant.sourceforge.net/). To ensure a high-quality dataset with minimal contaminating proteins from other subcellular compartments, proteins that were only found in the cytoplasmic fraction and never in the other two soluble fractions were used to assess PSORTb 3.0 and PA 3.0 prediction results. This dataset was also felt to be most appropriate for assessment, since our analysis had suggested that most proteins of previously unknown localization in the old version of PSORTb were most likely cytoplasmic proteins. Further details on the experimental protocols for this proteomics analysis of the subcellular fractions can be found in Supplementary Material—methods for mass spectrometry protein identification.
Publication 2010
Bacteria Cytoplasm Feelings Formaldehyde Gram Negative Bacteria Liquid Chromatography Mass Spectrometry Peptides Periplasm Proteins Proteome Proto-Oncogene Mas Pseudomonas aeruginosa Spectrometry Staphylococcal Protein A Subcellular Fractions Tandem Mass Spectrometry
A TSQ Quantum Ultra Plus triple-quadrupole mass spectrometer (Thermo Fisher Scientific, San Jose, CA, USA) equipped with an automated nanospray apparatus (i.e., Nanomate HD, Advion Bioscience Ltd., Ithaca, NY, USA) and Xcalibur system software were utilized in the study. Ionization voltages of −1.1, −0.95, and +1.2 kV and gas pressures of 0.3, 0.15, and 0.3 psi on the nanomate apparatus were employed for the analyses of anionic lipids, PtdEtn, and PtdCho, respectively. The nanomate was controlled by Chipsoft 7.2.0 software. Each lipid extract solution prepared above was properly diluted to less than 50 pmol of total lipids/μL with chloroform/methanol/isopropanol (1:2:4, v/v/v) prior to infusion into the mass spectrometer. This procedure was used to guarantee that no lipid aggregation occurred during analysis and to minimize any effects of residual inorganic components carried over during lipid extraction on ion suppression and/or chemical noise.
The first and third quadrupoles were used as independent mass analyzers with a mass resolution setting of 0.7 Thomson while the second quadrupole served as a collision cell for tandem mass spectrometry (MS/MS). Typically, a 1-min period of signal averaging in the profile mode was employed for each mass spectrum. For MS/MS, a collision gas pressure was set at 1.0 mTorr but the collision energy varied with the classes of lipids as described previously.4 (link),15 (link) For each MS/MS spectrum, a 2- to 5-min period of signal averaging in the profile mode was employed. All the MS spectra and MS/MS spectra were automatically acquired by a customized sequence subroutine operated under Xcalibur software. Data processing of MDMS analyses including ion peak selection, baseline correction, data transfer, peak intensity comparison, 13C de-isotoping, and quantitation were conducted using custom programmed Microsoft Excel macros, as outlined previously.15 (link)
Publication 2008
Cells Chloroform Isopropyl Alcohol Lipids Mass Spectrometry Methanol methylene dimethanesulfonate Pressure Spectrometry Tandem Mass Spectrometry
As input, proteiNorm
expects tab-separated peptide (optional) and protein data (not on
logarithmic scale) as produced by software such as MaxQuant,9 (link) where each row represents a peptide or protein
and the column names of the measured intensities (samples) beginning
with “Reporter intensity corrected” followed by an integer
and an optional label (e.g., “Reporter intensity corrected
5 TMT2”) for TMT experiments. The column names for samples
in label-free experiments should begin with “Intensity”
followed by an integer (“Intensity 01”). Data from both
mass spectrometry quantitation methods, tandem mass tag (TMT) and
label-free mass spectrometry, are supported. The TMT reporter intensities
should be corrected using the error correction factors provided by
Thermo Fisher for the specific TMT lot that was used during the sample
preparation. These correction factors are imported into MaxQuant when
setting up the database search parameters. The MaxQuant “proteinGroups.txt”
output file will then contain column names for each TMT reporter ion
labeled as “Reporter intensity corrected” and “Reporter
intensity”. In the following examples, we are using the “Reporter
intensity corrected” columns from MaxQuant since these intensities
apply the TMT correction factors. The reporter ion isotopic distributions
(−2, −1, +1, +2) are primarily for carbon isotopes with
reporter ion interference for each mass tag. ProteiNorm automatically
detects these column names and determines if the data is TMT or label-free
data type. ProteiNorm also removes proteins flagged as common contaminants
and reverse sequences in the MaxQuant output using the column names
“Potential contaminant” and “Reverse”
provided in the proteinGroups.txt MaxQuant output file. If you prefer
to load in a different matrix of data, then the column labels for
the samples will need to be modified to match the naming structure
provided here. An example of the data input files is hosted on Github
for both TMT and label-free data sets.
Due to the detection
limits of mass spectrometry instruments, many measurements of peptides
or proteins result in intensity levels of zero. These values will
be considered as missing values (denoted as NA) and can be imputed
with precaution. A modified heatmap of missing values (Figure 2C) from the DEP Bioconductor
package10 (link) helps to determine if data is
missing at random (MAR) or missing not at random (MNAR), and the MSnbase
vignette describes different imputation methods used for different
types of missing data.11 (link)
Publication 2020
Carbon Isotopes Isotopes Mass Spectrometry Peptides Proteins Spectrometry
LC-MSmass spectrometry (LC-MS/MS) is increasingly used in clinical settings for quantitative assay of small molecules and peptides such as vitamin D, serum bile acid and parathyroid hormone under Clinical Laboratory Improvement Amendments environments with high sensitivities and specificities34 . In this study, targeted metabolomic analysis of plasma samples was performed using the Biocrates Absolute-IDQ P180 (BIOCRATES, Life Science AG, Innsbruck, Austria). This validated targeted assay allows for simultaneous detection and quantification of metabolites in plasma samples (10 µL) in a high-throughput manner. The methods have been described in detail35 ,36 . The plasma samples were processed as per the instructions by the manufacturer and analyzed on a triple-quadrupole mass spectrometer (Xevo TQ-S, Waters Corporation, USA) operating in the MRM mode. The measurements were made in a 96-well format for a total of 148 samples, and seven calibration standards and three quality control samples were integrated in the kit. Briefly, the flow injection analysis tandem mass spectrometry (MS/MS) method was used to quantify a panel of 144 lipids simultaneously by multiple reaction monitoring. The other metabolites are resolved on the UPLC and quantified using scheduled MRMs. The kit facilitates absolute quantitation of 21 amino acids, hexose, carnitine, 39 acylcarnitines, 15 sphingomyelins, 90 phosphatidylcholines and 19 biogenic amines. Data analysis was performed using the MetIQ software (Biocrates), and the statistical analyses included the nonparametric Kruskal-Wallis test with follow-up Mann-Whitney U-tests for pairwise comparisons using the STAT pack module v3 (Biocrates). Significance was adjusted for multiple comparisons using Bonferroni’s method (P < 0.025). The abundance is calculated from area under the curve by normalizing to the respective isotope labeled internal standard. The concentration is expressed as nmol/L. Human EDTA plasma samples spiked with standard metabolites were used as quality control samples to assess reproducibility of the assay. The mean of the coefficient of variation (CV) for the 180 metabolites was 0.08, and 95% of the metabolites had a CV of <0.15.
Publication 2014
acylcarnitine Amino Acids Bile Acids Biogenic Amines Biological Assay Carnitine Clinical Laboratory Services Edetic Acid Ergocalciferol Flow Injection Analysis Hexoses Homo sapiens Hypersensitivity Isotopes Lipid A Parathyroid Hormone Peptides Phosphatidylcholines Plasma Serum Spectrometry Sphingomyelins Tandem Mass Spectrometry

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Publication 2013
Cells Mass Spectrometry Plasma Protoplasm Pyroptosis Spectrometry Tissue, Membrane Vision Yttrium

Most recents protocols related to «Spectrometry»

Example 4

Octadecanoate Functionalized Core (IMS 018 H)

To a round bottom flask was added one or more of the following “core” compounds: tripentaerythritol (“H”) made from the above cores. These were dissolved in tetrahydrofuran. 1.1 molar equivalents (per —OH of the hydroxyl terminated cores or dendrimers) of Octadecanoic Acid were added to the solution of cores. To these reagents were added 1.2 molar equivalents (per —OH of the hydroxyl terminated cores or dendrimers) of dicyclohexylcarbodiimide and 0.1 molar equivalents (per —OH of hydroxyl-terminated core or of dendrimer) of 4-dimethylaminopyridine (DMAP).

The reaction mixture was stirred vigorously for approximately 12 hours at standard temperature and pressure. The reaction was monitored by MALDI-TOF MS to determine completion of the reaction for each of the cores present in the reaction. After complete esterification is observed by MALDI-TOF MS, the flask contents were transferred to a separatory funnel, diluted with dichloromethane, extracted twice with 1M aqueous NaHSO4 (sodium bisulfate) and extracted twice with 1M aqueous NaHCO3 (sodium bicarbonate). The organic layer was reduced in vacuo to concentrate the sample. A MALDI-TOF MS spectra of the purified product confirmed the purity of the mixture of esterified products and is shown in FIG. 11.

FIG. 11 shows MALDI-TOF MS data for IMS 018 H, the product of octadecanoic acid functionalization of core H (IMS018H).

Patent 2024
4-dimethylaminopyridine Bicarbonate, Sodium Chromatography Dendrimers Dicyclohexylcarbodiimide Esterification Hydroxyl Radical Methylene Chloride Molar Pressure sodium bisulfate Spectrometry Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization Stearates stearic acid tetrahydrofuran

Example 7

Benzoate Functionalized Cores (IMS 100 C-F)

To a round bottom flask was added one or more of the following “core” compounds: tris(hydroxymethyl)ethane (“C”), pentaerythritol (“D”), xylitol (“E”), dipentaerythritol (“F”) made from the above cores. These were dissolved in tetrahydrofuran. 1.1 molar equivalents (per —OH of the hydroxyl terminated cores or dendrimers) of Benzoic Acid were added to the solution of cores. To these reagents were added 1.2 molar equivalents (per —OH of the hydroxyl terminated cores or dendrimers) of dicyclohexylcarbodiimide and 0.1 molar equivalents (per —OH of hydroxyl-terminated core or of dendrimer) of 4-dimethylaminopyridine (DMAP).

The reaction mixture was stirred vigorously for approximately 12 hours at standard temperature and pressure. The reaction was monitored by MALDI-TOF MS to determine completion of the reaction for each of the cores present in the reaction. After complete esterification is observed by MALDI-TOF MS, the flask contents were transferred to a separatory funnel, diluted with dichloromethane, extracted twice with 1M aqueous NaHSO4 (sodium bisulfate) and extracted twice with 1M aqueous NaHCO3 (sodium bicarbonate). The organic layer was reduced in vacuo to concentrate the sample. A MALDI-TOF MS spectra of the purified product confirmed the purity of the mixture of esterified products and is shown in FIG. 15.

FIG. 15 shows MALDI-TOF MS data for IMS 100 C-F, the product of benzoic acid functionalization of cores C, D, E, and F.

Patent 2024
4-dimethylaminopyridine Benzoate Benzoic Acid Bicarbonate, Sodium Chromatography Dendrimers Dicyclohexylcarbodiimide Esterification Ethane Hydroxyl Radical Methylene Chloride Molar pentaerythritol Pressure sodium bisulfate Spectrometry Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization tetrahydrofuran Tromethamine Xylitol
The solid catalyst was collected
from the water suspension by filtration under vacuum. The filter paper
with the black paste was dried at 20 °C by the airflow in a fume
hood. No inert gas protection was involved for catalyst handling or
transportation. The Ru and Pd contents in the catalysts were measured
by inductively coupled plasma–optical emission spectrometry
(ICP-OES, PerkinElmer Optima 8300) after digestion at the Microanalysis
Laboratory, University of Illinois at Urbana-Champaign. The oxidation
state of Ru and Pd was characterized by X-ray photoelectron spectroscopy
(XPS, Kratos AXIS Supra). The sp2 C 1s peak (284.5 eV)
of the carbon support was used for binding energy (BE) calibration.
XPS spectra in the resolution of 0.1 eV were fitted using CasaXPS
(version 2.3.19). Microscopic characterization was conducted using
scanning transmission electron microscopy (STEM, FEI Titan Themis
300) equipped with an energy-dispersive X-ray spectrometer (EDS) system.
The catalyst powder was resuspended and sonicated in distilled water
to further reduce the size. The STEM images were acquired with a high-angle
annular dark-field (HAADF) detector. Nano Measurer software package
was used for the statistical analysis of average particle size in
the STEM images. The specific surface areas of Ru and Pd were determined
by CO pulse titration experiments on a Quantachrome Autosorb-iQ physisorption–chemisorption
instrument. The calculation of metal dispersion used the surface Ru:CO
and Pd:CO stoichiometry of 12:741 (link) and 2:1,42 (link) respectively.
Publication 2023
Carbon Digestion Epistropheus Filtration Metals Microscopy Noble Gases Pastes Plasma Powder Pulse Rate Radiography Spectrometry Stem, Plant Titrimetry Transmission Electron Microscopy Vacuum Vision
All the
chemicals were purchased
from Sigma-Aldrich, Merk, Fisher
Scientific, or VWR and used as received. DOTA was purchased from MacrocyclicsTM.
DO2A-DipyNox is adopted from our previous studies,32 (link),33 (link) and was synthesized by Dr. Liu (present address: Fu Jen Catholic
University, New Taipei City, Taiwan). Solvents were purchased from
Honeywell, BIOSOLVE or Aldrich and stored over 3 Å molecular
sieves before use. Traces of water from reagents were removed by co-evaporation
with toluene in reactions that required anhydrous conditions. Flash
chromatography was performed on Screening Devices silica gel 60 (40–63
μm) and C18-reversed phase silica gel (fully endcapped, 40–63
μm). LC–MS analysis was performed on a Surveyor HPLC
system (Thermo Finnigan) equipped with a C18 column (Gemini, 4.6 mm
× 50 mm, 5 μm particle size, Phenomenex), coupled to an
LCQ Advantage Max (Thermo Finnigan) ion-trap spectrometer (ESI+).
Thin-layer chromatography (TLC) analysis was performed on a silica
gel (F 1500 LS 254 Schleicher and Schuell, Dassel, Germany), which
was visualized by UV and/or ninhydrin, KMnO4. Reactions
were monitored by LC–MS analysis and TLC analysis. Waters preparative
HPLC system, equipped with a Waters C18-Xbridge 5 μm OBD (30
× 150 mm2) column, was used for purification, and
the applied buffers were H2O (2% TFA) and ACN. High-resolution
mass spectrometry analysis was performed with an LTQ Orbitrap mass
spectrometer (Thermo Finnigan), equipped with an electron spray ion
source in a positive mode (source voltage 3.5 kV, sheath gas flow
10 mL/min, and capillary temperature 250 °C) with resolution R = 60,000 at m/z 400
(mass range m/z = 150–2000)
and dioctyl phthalate (m/z = 391.284)
as a “lock mass.” NMR spectra were recorded on a Bruker
AV-400 (400.130/100.613 MHz), AV-500 (500.130/125.758 MHz), or AV-HDIII-600
(600.130/150.903 MHz) spectrometer. Chemical shifts (δ) are
reported in ppm relative to the residual signal of the deuterated
solvent.
Publication 2023
Buffers Capillaries Diethylhexyl Phthalate Electrons Medical Devices Ninhydrin Silica Gel Solvents Spectrometry tetraxetan Thin Layer Chromatography Toluene

Reagent/resourceReference or sourceIdentifier or catalog
Bacterial strains
Mycobacterium bovis BCG PasteurAmerican Type Culture CollectionATCC 35748
M. bovis BCG gltBD transposon mutantVIB – Vlaams Instituut voor Biotechnologie(BCG_3922c TnInsertion‐8654)
Reagents
Middlebrook 7H11Merck Life ScienceM0428‐500G
Middlebrook 7H9Merck Life ScienceM0178‐500G
OADCBecton Dickenson212351 (4312351)
GlycerolMerck Life ScienceG7893‐1 L
TyloxapolMerck Life ScienceT8761‐50G
Brain heart infusion agarMerck Life Science70138‐500G
Rosins minimal mediaBeste et al (2011 (link))N/A
[13C3] glycerol, 99% purityCK IsotopesCLM‐1510‐5
[15N1] NH4Cl, 98% atom purityMerck Life Science299251
2 liter bioreactorElectrolabFermac 310/60
Peristaltic pumpRainin Rabbit PlusN/A
Gas analyzerElectrolabFermac 368
Glycerol assay kitMerck Life ScienceMAK117
Ammonia assay kitMerck Life ScienceMAK310
BCA assay kitMerck Life Science71285‐M
Ziehl neelsen stainMerck Life Science1.09215
Mass spectrometry equipment
tert‐butyldimethyl silyl chloride (TBDMSCl)Merck Life Science00942‐10ML
N‐Methyl‐N‐(trimethylsilyl)trifluoroacetamide, MSTFAMerck Life ScienceM‐132
GC–MS 7890‐5795AgilentBorah et al (2019 (link))
VF‐5 ms 30 m × 0.25 mm × 0.25 μm + 10 m EZ‐GuardAgilentCP9013
Dionex UltiMate system (HPLC)Thermo Fisher Scientific3000 RSLC
C18 and ZIC‐pHILIC column (150 mm × 4.6 mm, 5 μm column)Merck Sequant150461
Thermo Orbitrap Q Exactive PlusThermo Fisher ScientificN/A
Software
ChemstationAgilentN/A
GraphPad Prism 8.0GraphPad softwareN/A
Omix v.2.0.7Omix Visualization GmbH & Co.KG, Lennestadt/GermanyN/A
13CFLUX2 v2.2Weitzel et al (2013 (link))N/A
HOPS v2.0.0Jadebeck et al (2021 (link))N/A
Publication 2023
Biological Assay Chlorides Glycerin Heart High-Performance Liquid Chromatographies Jumping Genes prisma Rabbits Spectrometry TBDMSCl trifluoroacetamide

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More about "Spectrometry"

Spectrometry, also known as spectroscopy, is a powerful analytical technique that enables the identification and quantification of chemical compounds by measuring the interaction between matter and electromagnetic radiation.
This non-destructive method can be applied to a wide range of samples, from biological macromolecules to complex industrial mixtures.
Spectrometric techniques involve the separation of light into its constituent wavelengths, followed by the detection and analysis of the resulting spectrum.
These measurements provide valuable information about the chemical composition, structure, and properties of the analyte.
Spectrometry plays a crucial role in fields such as chemistry, physics, biology, and environmental science, facilitating advanced research, quality control, and diagnostic applications.
With continual advancements in instrumentation and data analysis, spectrometry remains an indispensable tool for scientists seeking to unveil the secrets of the physical world.
Spectrometers like the S-4800, Optima 8300, Optima 5300 DV, D8 Advance, and DU530 UV/VIS spectrophotometer are widely used in various applications, including the analysis of biological samples using reagents like TRIzol and the RNeasy Mini Kit.
Advanced spectrometric techniques, such as those employed by the ESCALAB 250Xi and Optima 8000, as well as electron microscopy instruments like the JEM-2100F, provide even deeper insights into the structure and properties of materials.
By leveraging the power of spectrometry, scientists can accelerate their research and drive breakthrough discoveries in diverse fields.