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Spectra manager software version 2

Manufactured by Jasco
Sourced in Japan

Spectra Manager software version 2 is a comprehensive data analysis and management tool designed for laboratory equipment. It provides advanced capabilities for processing, visualizing, and managing spectroscopic data from various instruments.

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7 protocols using spectra manager software version 2

1

CD Spectroscopy of Protein Folding

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CD spectra were recorded in 20 mM sodium phosphate at pH 7 and 150 mM NaCl, 20 mM sodium phosphate at pH 6 (with or without 150 mM NaCl) and 50 mM sodium acetate at pH 4 and 5, all containing 10 mM DPC at 20°C on a JASCO J-810 spectropolarimeter using Spectra Manager software version 2 (Jasco Analytical Instruments, Easton, MD) and a 0.1 cm path length flat cell. Temperature melting experiments were carried out by recording the CD signal at 222 nm as a function of increasing and decreasing temperature. α-helical content was determined using the CDNN program [44 (link)].
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2

Circular Dichroism Spectroscopy of SARS-CoV-2 Mpro Variants

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CD spectra were recorded using 10 μM protein in buffer B (25 mM Tris-HCl, pH 7, 50 mM NaCl and 1 mM TCEP) at 25°C on a JASCO J-810 spectropolarimeter using Spectra Manager software version 2 (Jasco Analytical Instruments, Easton, MD) and a 0.1 cm pathlength cell. Spectra were processed using the same software. The bandwidth was set to 1.0 nm with an integration time of 0.5 s and 100 nm/min scanning speed. Ten scans were averaged and subtracted from a buffer scan acquired the same way. For thermal denaturation measurements, the change in the CD signal at 222 nm was measured as a function of temperature from 25–60 °C for MProWT and MProH41A and 25–75 °C for MProC145A at 1 °C intervals. The spectra were normalized to the mean residue ellipticity.
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3

CD Spectroscopy of Biomolecules

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CD spectra were recorded in buffer B at 25 °C on a JASCO J-810 spectropolarimeter using Spectra Manager software version 2 (Jasco Analytical Instruments, Easton, MD) and a 0.1 cm pathlength cell. Spectra were processed using the same software.
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4

FTIR Analysis of Material Samples

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The spectral measurements were made with a UV-Vis Perkin-Elmer Lambda25 and an FTIR Jasco 6300 spectrometer.
An ATR accessory equipped with a diamond crystal (Pike Technologies, Madison, Wisconsin, USA) allows the collection of FTIR spectra directly on a sample without any special preparation. The FTIR spectra were recorded in the region of 4000–400 cm−1, with a TGS detector, and apodization Cosine. The spectral data were processed with JASCO Spectra Manager software, version 2. Samples were scanned at a 4 cm−1 resolution, accumulation: 100 scans. Background reference spectra were recorded using air after every sample to minimize the interference due to carbon dioxide and water vapor in the atmosphere. Between measurements, the ATR crystal was carefully cleaned using pure acetone (Sigma-Aldrich Co., Saint Louis, MO, USA), then, it was dried with soft tissue [43 (link),44 (link),45 (link)].
All measurements were taken at room temperature (T = 23 °C). For each sample, three replicate spectra were recorded to ensure spectral reproducibility and to assess analytical precision; then, the average spectrum was complete.
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5

Thermal Stability of SARS-CoV-2 Mpro Variants

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CD spectra were recorded using 10 µM protein in buffer B (25 mM Tris-HCl, pH 7, 50 mM NaCl and 1 mM TCEP) at 25 °C on a JASCO J-810 spectropolarimeter using Spectra Manager software version 2 (Jasco Analytical Instruments, Easton, MD) and a 0.1 cm pathlength cell. Spectra were processed using the same software. The bandwidth was set to 1.0 nm with an integration time of 0.5 s and 100 nm/min scanning speed. Ten scans were averaged and subtracted from a buffer scan acquired the same way. For thermal denaturation measurements, the change in the CD signal at 222 nm was measured as a function of temperature from 25-60 °C for MProWT and MProH41A and 25–75 °C for MProC145A at 1 °C intervals. The spectra were normalized to the mean residue ellipticity.
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6

Spectrophotometric Analysis of Samples

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JASCO V-650 spectrophotometer and a 1 cm quartz cell were utilized for scanning the D0 spectra. Spectra manager® software, version 2, JASCO corporation was used to handle absorption and derivative ratio spectra.
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7

Seaweed FTIR Spectroscopic Analysis

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A ZnSe 45° HATR (horizontal attenuated total reflectance) crystal (PIKE Technologies, Madison, WI, USA) and an FTIR-6200 JASCO spectrometer (Jasco Corp., Tokyo, Japan) equipped with a standard sample chamber, a triglycine sulphate (TGS) detector and a Ge/KBr beam splitter was used for the acquisition of spectral data. A small quantity of each seaweed sample was cut into small pieces, placed onto the crystal surface and pressed with a gripper to ensure the best possible contact with the crystal. The crystal used shows a refractive index of 2.4 and a depth of penetration of 2.0 µm at 1000 cm−1. The spectra were obtained from the range of 4000 to 400 cm−1 by accumulating 100 scans with a resolution of 4 cm−1 and a total integration time of 2 min using Spectra Manager™ software version 2 (Jasco Corp., Tokyo, Japan). In total, 351 samples were spectroscopically analyzed, while 171 and 180 of them originated from MI and SAMS, respectively.
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