The largest database of trusted experimental protocols

Opus v6

Manufactured by Bruker
Sourced in Germany, United States

OPUS V6.5 is a comprehensive software suite for data acquisition, processing, and analysis of infrared and Raman spectroscopic data. It provides a wide range of tools and algorithms for spectral manipulation, multivariate analysis, and visualization.

Automatically generated - may contain errors

20 protocols using opus v6

1

FTIR Analysis of BECC438 and BECC470 Thermal Transitions

Check if the same lab product or an alternative is used in the 5 most similar protocols
For infrared measurements, 20 mM BECC438 and 20 mM BECC470 were prepared in 10 mM HEPES buffer at pH 7. The suspensions were heated at 70 °C in a water bath for 5 min and then cooled down to 4 °C for 10 min for three cycles [18 (link),19 (link)]. The samples were stored at 4 °C prior to obtaining measurements. FTIR spectroscopic analysis was performed using a Tensor-27 FTIR spectrometer (Bruker, Billerica, MA) equipped with a Bio-ATR cell. The detector was cooled with liquid N2 for 20 min prior to use, and the interferometer was purged continuously with N2 gas. A total of 256 scans were recorded from 4000 to 900 cm−1 with a 4 cm−1 resolution. Buffer background spectra were collected and subtracted from the sample spectra. Atmospheric compensation and baseline adjustment were applied using OPUS V6.5 software (Bruker, Billerica, MA). Thermal transition experiments were performed with the temperature ramped from 25 °C to 95 °C at increments of 2.5 °C per step and an equilibration time of 2 min at each temperature. The thermal transition curves were constructed by plotting the frequency shift at 2850 cm−1 as a function of temperature. The absorption at 2850 cm−1 indicates the methylene symmetric (svCH2) stretching mode [20 (link),21 (link)].
+ Open protocol
+ Expand
2

Infrared Spectroscopy of Polymer Gelation

Check if the same lab product or an alternative is used in the 5 most similar protocols
Infrared spectra were recorded on an ALPHA FT-IR spectrometer (Bruker) and analyzed using OPUS v. 6.5 software (Bruker). Spectra were recorded at several time points during gel formation. Each time point represents an aliquot taken from a single continual polymerization and was directly measured on the ZnSe ATR crystal as either a liquid, gel, suspension or solid depending on the time at which the sample was measured. For example, at 15 min the polymerization was not crosslinked and still a liquid, therefore the liquid was directly dispensed on the crystal but at 600 min the mixture was a solid, thus a thin slab of polymer was directly placed on the crystal. Background spectra were recorded between samples and the crystal was cleaned with isopropanol.
+ Open protocol
+ Expand
3

Salivary Infrared Spectroscopy

Check if the same lab product or an alternative is used in the 5 most similar protocols
Salivary spectra were recorded in the transmission mode (OPUS v.6.5 software, Bruker) using ATR-FTIR spectrophotometer Vertex 70 (Bruker Optics) using a micro-attenuated total reflectance (ATR) component. The Eppendorf devices with saliva were inserted in a vortex for 5 min to homogenate the sample, and 2 μL were collected and directly dried on ATR-crystal with a dry dentistry airflow for 5 min for infrared spectra recording. Spectra were acquired with 4 cm−1 spectral resolution and 32 scans per sample, from 400 to 4000 cm−1. Two replicates per sample were studied and the mean was used for each sample [21 (link),23 (link),31 (link)].
+ Open protocol
+ Expand
4

FTIR Spectroscopy of Plasma Samples

Check if the same lab product or an alternative is used in the 5 most similar protocols
The sample preparation and acquisition methodology for FTIR spectra was detailed in our previous paper [18] . Briefly, plasma samples stored at -80° C were thawed at room temperature and were diluted threefold in physiological water. A volume of 4 μL diluted plasma sample was deposited on a 384-well silicon plate (Bruker Optics GmbH, Ettlingen, Germany), and air-dried at room temperature. For each sample, 10 spots were used giving 10 instrumental replicates. The plate was then inserted into a high-throughput module (HTS-XT, Bruker Optics GmbH) attached to an FTIR spectrometer (Tensor 27, Bruker Optics GmbH). FTIR spectra were acquired in the transmission mode using the OPUS v6.5 software (Bruker Optics GmbH) in the wavenumber range from 4000 to 400 cm -1 , using a spectral resolution of 4 cm -1 and 32 co-additions. FTIR spectra were then subjected to a quality test (OPUS v6.5) and details of this test are fully described in reference [19, 20] . Spectra that passed the quality test were pre-processed and processed in the wavenumber range from 800 to 4000 cm -1 .
+ Open protocol
+ Expand
5

FTIR Analysis of Protein Samples

Check if the same lab product or an alternative is used in the 5 most similar protocols
FTIR analysis was performed using a Tensor-27 FTIR spectrometer (Bruker, Billerica, MA). For protein concentrations and buffers for each mAb, see Table 1. Protein samples were measured from 800 – 4000 cm−1 with a resolution of 4 cm−1. A total of 256 scans were performed for both samples and buffers at 25 °C. For the thermal melting experiments, 64 scans were obtained, and samples were scanned from 25 to 90 °C using an increment of 2.5 °C/step and an equilibration time sufficient to reach equilibrium (2 min) at each step. Buffer subtraction, water vapor and CO2 compensation, baseline correction, and normalization of the amide I band (1700 – 1600 cm−1) were sequentially performed on the raw FTIR spectra using the OPUS V6.5 software (Bruker, Billerica, MA). Second derivative FTIR spectra were generated using a Savitzky–Golay filter with a window size of 9.
The bend + liberation FTIR band of water in these protein samples and their buffers were measured by using air as the blank. Samples were scanned from 800 to 4000 cm−1 using a resolution of 2 cm−1. A total of 256 scans were performed. λμ was calculated between 1900 and 2300 cm−1 for the water band.
+ Open protocol
+ Expand
6

FTIR Spectroscopy Quality Control

Check if the same lab product or an alternative is used in the 5 most similar protocols
Spectra were collected with a high-throughput module (HTS-XT) coupled to a FTIRspectrometer (Tensor 27, Bruker Optics GmbH, Ettlingen, Germany). The spectral acquisition was performed in the transmission mode (OPUS v.6.5 software, Bruker Optics GmbH) in the 4000-400 cm -1 range with a spectral resolution of 4 cm -1 and 32 co-added scans. For each sample, a background was recorded and automatically removed to obtain the final absorbance spectrum. A spectral quality test (QT) as previously described [11, 13] was applied to each spectrum, which resulted in 1.4% of serum spectra and 0.7% of plasma spectra that were discarded. All raw spectra that passed the quality test are presented in Figure S2. However, it has been observed that among them 3.2% of serum and 0.3% of plasma spectra, all from experiments performed with a RH above 50%, had a non-strictly increasing absorbance in the spectral region 3700-3320 cm -1 (Figure S3). This translates a high content of water in the sample replicates, and this level has been chosen as a maximum threshold. These spectra were computationally discarded based on their 2 nd derivative form exhibiting peaks not present in other spectra at 3530, 3510, 3484, 3450 and 3420 cm -1 .
+ Open protocol
+ Expand
7

FT-IR Spectroscopic Analysis of Protein Structure

Check if the same lab product or an alternative is used in the 5 most similar protocols
A Tensor-27 FT-IR spectrometer (Bruker, Billerica, MA) equipped with a Bio-ATR cell was used for FT-IR spectroscopic analysis. Liquid nitrogen was used to cool the detector and a continuous N2 gas flow was used to purge the interferometer. A total of 256 scans were recorded from 4000 to 900 cm−1 at a 4 cm−1 resolution at 10 °C. The background spectra from each experimental buffer condition were subtracted from the sample spectra. Acquired spectra were processed for atmospheric compensation, baseline adjustment, and normalization by OPUS V6.5 (Bruker, Billerica, MA) software. Deconvolution of the amide I region of the acquired spectra from various experimental conditions were performed by Python script where the data set was processed by mixed Gaussian/Lorentzian bands. Similarly, the second derivative of each spectrum was calculated, and peaks were identified for secondary structure content.
+ Open protocol
+ Expand
8

FT-IR Analysis of Protein Thermal Unfolding

Check if the same lab product or an alternative is used in the 5 most similar protocols
FT-IR spectroscopic analysis was performed using a Tensor-27 FT-IR spectrometer (Bruker, Billerica, MA) equipped with a Bio-ATR cell. The detector was cooled with liquid N2 for 20 min prior to use and the interferometer was purged continuously with N2 gas. A total of 256 scans were recorded from 4000 to 900 cm−1 with a 4 cm−1 resolution. Buffer/emulsion background spectra were collected and subtracted from the sample spectra. Atmospheric compensation, baseline adjustment and second derivative calculations were applied using OPUS V6.5 (Bruker, Billerica, MA) software. To compare the initial state of the samples, spectra collected at 20 °C were deconvoluted into a set of mixed Gaussian/Lorentzian bands, using the build-in Levenberg-Maquardt algorithm from the OPUS V6.5 software. Thermal unfolding experiments were performed with the temperature ramped from 20 to 90 °C or 99 °C (for AT in SE) at increments of 2.5 °C per step and an equilibration time of 2 min at each temperature. The second derivative of each spectrum was calculated with nine point smoothing. The thermal unfolding curves of AT were constructed by plotting the second derivative signal at 1621 cm−1 (an indication of intermolecular β-structure and protein aggregation) as a function of temperature. The melting temperature (Tm) was calculated by a first derivative method using Origin 2017 (OriginLab; Northampton, MA).
+ Open protocol
+ Expand
9

FT-IR Spectroscopic Analysis of Protein Structure

Check if the same lab product or an alternative is used in the 5 most similar protocols
A Tensor-27 FT-IR spectrometer (Bruker, Billerica, MA) equipped with a Bio-ATR cell was used for FT-IR spectroscopic analysis. Liquid nitrogen was used to cool the detector and a continuous N2 gas flow was used to purge the interferometer. A total of 256 scans were recorded from 4000 to 900 cm−1 at a 4 cm−1 resolution at 10 °C. The background spectra from each experimental buffer condition were subtracted from the sample spectra. Acquired spectra were processed for atmospheric compensation, baseline adjustment, and normalization by OPUS V6.5 (Bruker, Billerica, MA) software. Deconvolution of the amide I region of the acquired spectra from various experimental conditions were performed by Python script where the data set was processed by mixed Gaussian/Lorentzian bands. Similarly, the second derivative of each spectrum was calculated, and peaks were identified for secondary structure content.
+ Open protocol
+ Expand
10

Spectroscopic Characterization of rGH-IONP Interactions

Check if the same lab product or an alternative is used in the 5 most similar protocols
Spectra of rGH solutions (1 mg/mL) with varying concentrations of IONPs (0.42 to 1.47 mM) were acquired with a Bruker Tensor 27 FTIR spectrometer fitted with a Bio-ATR cell (Bruker, Billerika, MA). Scans were recorded from 600 to 4000 cm−1 at a resolution of 1 cm−1. The FTIR spectra were acquired after 10 min, 30 min, 1 h and 2 h incubation periods at ambient temperature. In addition, rGH and rGH-IONP mixtures were incubated at increasing temperatures from 15 to 85 °C at increments of 2.5 °C/step with a 120 s equilibration time, and 128 scans/step. The phosphate buffer-IONP-mixture was used for background subtraction of the FTIR spectra. The Salvitzky-Golay algorithm was used to calculate the second derivative spectra, baseline and atmospheric corrections, and 9-point data smoothing (Opus v6.5, Bruker Corporation, Billerica, MA).
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!