Spectrometry
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»
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 (
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)
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
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
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.
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.
Reagent/resource | Reference or source | Identifier or catalog |
---|---|---|
Mycobacterium bovis BCG Pasteur | American Type Culture Collection | ATCC 35748 |
M. bovis BCG gltBD transposon mutant | VIB – Vlaams Instituut voor Biotechnologie | (BCG_3922c TnInsertion‐8654) |
Middlebrook 7H11 | Merck Life Science | M0428‐500G |
Middlebrook 7H9 | Merck Life Science | M0178‐500G |
OADC | Becton Dickenson | 212351 (4312351) |
Glycerol | Merck Life Science | G7893‐1 L |
Tyloxapol | Merck Life Science | T8761‐50G |
Brain heart infusion agar | Merck Life Science | 70138‐500G |
Rosins minimal media | Beste et al (2011 (link)) | N/A |
[13C3] glycerol, 99% purity | CK Isotopes | CLM‐1510‐5 |
[15N1] NH4Cl, 98% atom purity | Merck Life Science | 299251 |
2 liter bioreactor | Electrolab | Fermac 310/60 |
Peristaltic pump | Rainin Rabbit Plus | N/A |
Gas analyzer | Electrolab | Fermac 368 |
Glycerol assay kit | Merck Life Science | MAK117 |
Ammonia assay kit | Merck Life Science | MAK310 |
BCA assay kit | Merck Life Science | 71285‐M |
Ziehl neelsen stain | Merck Life Science | 1.09215 |
tert‐butyldimethyl silyl chloride (TBDMSCl) | Merck Life Science | 00942‐10ML |
N‐Methyl‐N‐(trimethylsilyl)trifluoroacetamide, MSTFA | Merck Life Science | M‐132 |
GC–MS 7890‐5795 | Agilent | Borah et al (2019 (link)) |
VF‐5 ms 30 m × 0.25 mm × 0.25 μm + 10 m EZ‐Guard | Agilent | CP9013 |
Dionex UltiMate system (HPLC) | Thermo Fisher Scientific | 3000 RSLC |
C18 and ZIC‐pHILIC column (150 mm × 4.6 mm, 5 μm column) | Merck Sequant | 150461 |
Thermo Orbitrap Q Exactive Plus | Thermo Fisher Scientific | N/A |
Chemstation | Agilent | N/A |
GraphPad Prism 8.0 | GraphPad software | N/A |
Omix v.2.0.7 | Omix Visualization GmbH & Co.KG, Lennestadt/Germany | N/A |
13CFLUX2 v2.2 | Weitzel et al (2013 (link)) | N/A |
HOPS v2.0.0 | Jadebeck et al (2021 (link)) | N/A |
Top products related to «Spectrometry»
More about "Spectrometry"
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.