Spectra analysis software

Manufactured by Jasco

Sourced in United States

Spectra Analysis software is a data analysis tool designed to process and interpret spectral data. It provides essential functions for visualizing, manipulating, and analyzing various types of spectral information without extrapolation on intended use.

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Lab products found in correlation

J 820 spectropolarimeter, by Jasco (2 mentions) J 815 spectropolarimeter, by Jasco (2 mentions) Cary 300 bio, by Agilent Technologies (1 mentions) J 815 circular dichroism spectropolarimeter, by Jasco (1 mentions) Suprasil, by Hellma (1 mentions) J 720, by Jasco (1 mentions) J 1500 cd spectrophotometer, by Jasco (1 mentions) 1 mm quartz cuvettes, by Thermo Fisher Scientific (1 mentions) Quartz high precision cell, by Hellma (1 mentions) J 815, by Jasco (1 mentions) Black walled 96 well plate, by Corning (1 mentions) J 715 spectrophotometer, by Jasco (1 mentions) J 810 cd spectrophotometer, by Jasco (1 mentions) Quartz cuvette, by Hellma (1 mentions) J 815 cd spectrometer, by Jasco (1 mentions)

Spelling variants of this product

Spectra Analysis (6 citations) Jasco Spectra-Manager Analysis Software (2 citations)

18 protocols using spectra analysis software

Analyzing Dental Mineralization by ATR-IR

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The same dentine samples that were analyzed by EDX were submitted for ATR-IR surface analyses by a Bruker Alpha (Bruker Optik GmbH, Ettlingen, Germany) Fourier-Transform FT-IR spectrometer in ATR mode with a diamond inner reflection element (IRE). The I_apatite/I_{amide II} and I_{1410(carbonate)}/I_{554(phosphate)} absorbance ratios were calculated as peak heights by using the Jasco Spectra analysis software (Jasco Inc., Easton, MD, USA), version 1.53.03. At least three spectra were recorded for each sample at each step of the study. Average spectra were shown; I_apatite/I_{amide II} and I_{1410(carbonate)}/I_{554(phosphate)} values were reported as mean values ± standard deviation.
The reduction of the I_apatite/I_{amide II} ratio indicated the occurrence of a demineralization, with the weakening of the apatite bands compared to those of collagen while increasing the ratio indicated a remineralization. The changes in the I_{1410(carbonate)}/I_{554(phosphate)} ratio assessed the carbonate content of the B-type carbonated apatite. The shifts of the collagen bands (Amide II e III) allowed for evaluation of the collagen rearrangements. Under the used experimental conditions, the penetration into the sample thickness was about 2 µm.

Gandolfi M.G., Taddei P., Pondrelli A., Zamparini F., Prati C, & Spagnuolo G. (2018). Demineralization, Collagen Modification and Remineralization Degree of Human Dentin after EDTA and Citric Acid Treatments. Materials, 12(1), 25.

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Spectroscopic Characterization of Species

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The absorption spectra in the UV–vis region were recorded
at 298 K on a Cary300 Bio (Varian) spectrophotometer in 1 cm path
length quartz cells. CD spectra were recorded on a Jasco J 715 spectropolarimeter
over the range of 220–800 nm using different path lengths (1
and 0.1 cm). Sample solutions for UV–vis and CD spectroscopic
studies had compositions similar to those employed in the potentiometric
experiments. All measurements were recorded in the pH range of 2.5–11.5.
The pH was adjusted with appropriate amounts of HCl and NaOH solutions.
Absorptivities (ε, M^–1 cm^–1) were calculated at the pH value of the maximum concentration of
the considered species, as indicated by the potentiometric distribution
diagrams. All of the used solutions in this study were deaerated.
CD spectra were analyzed using Jasco Spectra Analysis Software (version
1.53.04). Data were processed using Origin 7.0.

Peana M., Gumienna-Kontecka E., Piras F., Ostrowska M., Piasta K., Krzywoszynska K., Medici S, & Zoroddu M.A. (2020). Exploring the Specificity of Rationally Designed Peptides Reconstituted from the Cell-Free Extract of Deinococcus radiodurans toward Mn(II) and Cu(II). Inorganic Chemistry, 59(7), 4661-4684.

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Structural Analysis of IgG1-Fc and MBP-Fc by CD

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To analyze the
secondary structures
of Expi293-derived IgG1-Fc and MBP-Fc, the circular dichroism (CD)
spectra were recorded with a J-820 spectropolarimeter (Jasco) using
the samples prepared at 0.1 mg/mL in PBS (pH 7.4) at 25 °C. The
CD measurements were performed at a scanning speed of 20 nm/min by
continuous scanning from 260 to 200 nm using a 1 mm path-length quartz
cell. Five scans were recorded for each sample, and the collected
data were analyzed by Spectra Analysis software (Jasco).

Kosuge H., Nagatoishi S., Kiyoshi M., Ishii-Watabe A., Terao Y., Ide T, & Tsumoto K. (2022). Biophysical Characterization of the Contribution of the Fab Region to the IgG-FcγRIIIa Interaction. Biochemistry, 62(2), 262-269.

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Circular Dichroism Analysis of Collagen

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The CD analysis was performed on N-COL as provided and after being dissolved in 40%AA (20N-COL). The 20N-COL sample was prepared as in Section 2.1.1, transferred into a 5 mL Eppendorf, frozen at −20 °C overnight and then lyophilized under vacuum (<0.1 mbar) for 24 h. Then, 5 mg of each sample (N-COL and 20N-COL) was added to 5 mL of ddH₂O under stirring at room temperature, attaining a concentration of 1 mg/mL. To avoid the signal saturation (absorbance higher than 1.0), a calibration step was performed for each sample where collagen was diluted up to a concentration of 0.1 mg/mL. The CD analysis was performed on diluted samples (0.1 mg/mL), using a JASCO J-815 Circular Dichroism Spectropolarimeter, equipped with a Xe arc lamp, to record data in the far-UV spectral range. A total number of 3 scans were recorded for each sample at 50 nm/sec scanning rate and at 20 °C to obtain the final averaged CD spectra, and the data analysed with the Spectra Analysis software, purchased by JASCO. All the tests were performed using a quartz circular cuvette with a path length of 0.1 mm in the 180–260 nm wavelength range. Correction of spectra were performed considering the correspondent solvent medium as baseline (ddH₂O).

Melo P., Montalbano G., Boggio E., Gigliotti C.L., Dianzani C., Dianzani U., Vitale-Brovarone C, & Fiorilli S. (2022). Electrospun Collagen Scaffold Bio-Functionalized with Recombinant ICOS-Fc: An Advanced Approach to Promote Bone Remodelling. Polymers, 14(18), 3780.

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Characterization of Yeast SOD1 Oxidation

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Far-UV (178 − 260 nm) CD spectra were collected at 25 °C on a Jasco J-815 spectropolarimeter equipped with a Peltier-element-controlled thermostat. All CD measurements were performed with a spectral bandwidth of 2 nm, a digital integration time of 4 s, and a scanning speed of 20 nm min⁻¹ using a 50 μm path length cell. The final spectrum was obtained by subtracting the spectrum of the sample buffer (20 mM MOPS-NaOH buffer, pH 7.4) from the mean sample spectrum of three individual scans using Jasco Spectra Analysis software, with a Savitzky-Golay algorithm of convolution width 11 applied.
SDS-PAGE was employed to examine oxidation-induced oligomerization. Control samples were collected at 0.1 min and 180 min and compared to ySOD1 incubated with Cu²⁺, H₂O₂, AscH⁻, and EDTA alone for 180 min, or aliquots from complete reaction systems collected at 0.1, 3, 5, 15, 30, 60, and 180 min. Sample containing 37.5 μM ySOD1 were heated to 95 °C for 10 min. Molecular mass markers (Invitrogen pre-stained marker 161–036) and samples were electrophoresed using 4–12% NuPAGE Bis-Tris mini acrylamide gels (Invitrogen, Carlsbad, CA, USA), using the suppliers’ protocol (200 V, 40 min) and stained with Coomassie Brilliant Blue.

Tiwari M.K., Hägglund P.M., Møller I.M., Davies M.J, & Bjerrum M.J. (2019). Copper ion / H2O2 oxidation of Cu/Zn-Superoxide dismutase: Implications for enzymatic activity and antioxidant action. Redox Biology, 26, 101262.

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Circular Dichroism Spectroscopy Protocol

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CD spectra were recorded on a Jasco J-815 spectrophotometer between 400 and 180 nm at 0.1 nm intervals, using 1 mm Suprasil® (Hellma) quartz cuvettes at 25 °C. Three consecutive scans at a scan-rate of 10 nm/min, 8 s response time and 1 nm bandwidth were averaged for each sample and for the background spectra. After subtracting the appropriate background spectra, the corrected CD data were processed using Jasco Spectra Analysis software.

Babii O., Afonin S., Schober T., Komarov I.V, & Ulrich A.S. (2017). Flexibility vs rigidity of amphipathic peptide conjugates when interacting with lipid bilayers. Biochimica et Biophysica Acta, 1859(12), 2505-2515.

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Circular Dichroism Analysis of EptA Protein

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The folded state of WT and mutant EptA was confirmed following buffer exchange into 20 mM sodium phosphate pH 7.0, 3× CMC detergent (0.023% DDM or 0.14% DPC) with a 5 ml HisTrap Desalting Column using an ÅKTApurifier FPLC system and diluted to a concentration of 0.1 mg ml⁻¹. The far- UV spectral region was measured at 20°C on a circular dichroism (CD) spectrophotometer (Jasco J-720) using a 1 mm path length quartz cuvette. Data were collected every 1 nm in the 190–260 nm wavelength region with an integration time of 1 s per step and three accumulations. The CD spectra were collected in triplicate, corrected for the buffer baseline and the signal-to-noise ratio was improved using a Savitzky–Golay filter with the minimum convolution width (of five data points) using Spectra Analysis software (version 1.53.07 for Windows 95/NT, Jasco Corp.).

Anandan A., Dunstan N.W., Ryan T.M., Mertens H.D., Lim K.Y., Evans G.L., Kahler C.M, & Vrielink A. (2021). Conformational flexibility of EptA driven by an interdomain helix provides insights for enzyme–substrate recognition. IUCrJ, 8(Pt 5), 732-746.

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Circular Dichroism Analysis of mAb Structure

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The secondary structure of each mAb was analyzed by the measurement of the circular dichroism (CD) spectrum using a J‐820 spectropolarimeter (Jasco). Samples were prepared at 0.7 μM in PBS (pH 7.4) in a 1 mm path‐length quartz cell. The CD measurements were carried out at 25°C by continuous scanning from 200 to 260 nm at a scanning speed of 20 nm/min. Five scans of each sample were accumulated. Analysis of the collected data was carried out using Spectra Analysis software (Jasco).

Kosuge H., Nagatoishi S., Kiyoshi M., Ishii‐Watabe A., Tanaka T., Terao Y., Oe S., Ide T, & Tsumoto K. (2020). Highly sensitive HPLC analysis and biophysical characterization of N‐glycans of IgG‐Fc domain in comparison between CHO and 293 cells using FcγRIIIa ligand. Biotechnology Progress, 36(6), e3016.

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Circular Dichroism Analysis of Protein Thermostability

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The secondary structure and thermostability of protein complexes were investigated using circular dichroism (CD) spectroscopy on J-1700 Circular Dichroism Spectrophotometer. The protein complexes were prepared in a phosphate buffer (consisting of pH 8.0, 3.52 mM KH₂PO₄, 46.48 mM K₂HPO₄, 50 mM K₂SO₄, 2 mM LDAO and 1 mM DPC) for analysis at room temperature using Spectra Analysis software (JASCO) and for variable temperature CD analysis using the temperature interval measurement function on the JASCO instrument.
The spline interpolation method was used to compute the areas between the two temperature–CD curves (25 °C and 95 °C) to quantify the thermostability. In addition, the curve variation magnitudes represented by delta mean residue ellipticity were examined using both the Friedman nonparametric hypothesis test and Kendall’s coefficient of concordance, as both methods are highly suited to non-normally distributed data as nonparametric tests.

Wang Z., Ding W., Ruan M., Liu Y., Yang J., Zhang H., Shen B., Wang J, & Li Y. (2023). NMR and Patch-Clamp Characterization of Yeast Mitochondrial Pyruvate Carrier Complexes. Biomolecules, 13(5), 719.

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Circular Dichroism Analysis of PBRM1-BD4

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PBRM1-BD4 secondary structure was assessed using a J-1500 CD spectrophotometer (JASCO). The samples were prepared at a concentration of 0.4 mg/ml in buffer (50 mM Na₃PO₄, 200 mM NaF, 5% v/v glycerol, pH 7.5 at 20 °C) and placed in 1 mm quartz cuvettes (Thermo Fisher Scientific). CD spectra were recorded at 25 °C from 280 to 200 nm, with a data pitch of 0.1 nm. A bandwidth of 1 nm was used with a digital integration time of 1 s and a scanning speed of 50 nm/min. Each spectrum was accumulated from five scans and corrected by subtracting the buffer spectrum from the sample spectrum. The data was processed using Spectra Analysis software supplied by the manufacturer (JASCO, https://jascoinc.com/products/spectroscopy/molecular-spectroscopy-software/) and transferred to GraphPad Prism for presentation.

Bursch K.L., Goetz C.J., Jiao G., Nuñez R., Olp M.D., Dhiman A., Khurana M., Zimmermann M.T., Urrutia R.A., Dykhuizen E.C, & Smith B.C. (2024). Cancer-associated polybromo-1 bromodomain 4 missense variants variably impact bromodomain ligand binding and cell growth suppression. The Journal of Biological Chemistry, 300(4), 107146.

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