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Decyder software version 6

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DeCyder software version 6.5 is a bioinformatics tool designed for the analysis of protein expression data generated from two-dimensional differential gel electrophoresis (2D-DIGE) experiments. The software provides automated spot detection, quantification, and statistical analysis of protein abundance changes across multiple samples.

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Lab products found in correlation

Imagequant tl software, by GE Healthcare (4 mentions) Typhoon trio, by GE Healthcare (3 mentions) Prism 4, by GraphPad (1 mentions) Decyder software, by GE Healthcare (1 mentions) Ettan spot picker, by GE Healthcare (1 mentions) 2 d quant kit, by GE Healthcare (1 mentions) Typhoon trio, by Cytiva (1 mentions)

Close spelling variants of this product

DeCyder software (30 citations) DeCyder 6.5 (13 citations) DeCyder version 6.5 software (5 citations)

7 protocols using decyder software version 6

1

Quantitative Proteome Analysis of Spinal Cord

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Total proteins were extracted and purified from fresh spinal cord tissues (L5) of Lv-PKIA-AS1 infected mice and the control mice using a ReadyPrepTM Protein Extraction kit (Bioscience) following the procedure recommended by the manufacturer. The proteomics analysis was performed as previously described (Yang et al., 2014 (link)). Protein samples were separated by two-dimensional polyacrylamide gel electrophoresis (2-DE). Samples containing 150 μg of protein were diluted to 450 μl with rehydration solution and used for isoelectric focusing. The proteins were electrophoresed in SDS–PAGE and then stained with coomassie brilliant blue dye. Spot-detect and determine the quantity were analyzed by DeCyder software version 6.5 (GE). The statistical significance was assessed by using a one-way ANOVA analysis. Protein spots were selected as the mean ratio was greater than 1.5-fold or less than -1.5-fold.
Hu J.Z., Rong Z.J., Li M., Li P., Jiang L.Y., Luo Z.X., Duan C.Y., Cao Y, & Lu H.B. (2019). Silencing of lncRNA PKIA-AS1 Attenuates Spinal Nerve Ligation-Induced Neuropathic Pain Through Epigenetic Downregulation of CDK6 Expression. Frontiers in Cellular Neuroscience, 13, 50.
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2

SDS-PAGE Image Analysis Protocol

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Image scans were carried out immediately following the SDS-PAGE using Typhoon TRIO (GE Healthcare) following the manufacture’s protocol. Scanned images were analyzed by Image QuantTL software (GE-Healthcare) and subjected to in-gel analysis and cross-gel analysis using DeCyder software version 6.5 (GE-Healthcare). Spots with either protein score or total Ion (C.I. %) greater than 95 were considered significant and protein candidates were randomly selected for spot picking.
Feugang J.M., Liao S.F., Willard S.T, & Ryan P.L. (2018). In-depth proteomic analysis of boar spermatozoa through shotgun and gel-based methods. BMC Genomics, 19, 62.
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3

Statistical Analysis of Proteomic Data

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One-tailed and two-tailed Student’s t tests, one-way ANOVA, Tukey’s multiple comparison
test, and Dunnett’s test were performed using Prism 4 (GraphPad
Software, Inc.). For proteomics expression comparisons, Decyder software,
version 6.5 (GE Healthcare Bio-Sciences) was used. Statistical significance
was taken to be p < 0.05 unless otherwise noted.
Treatment groups consisted of n = 5 unless otherwise
noted.
Dennis K.E, & Valentine W.M. (2015). Ziram and Sodium N,N-Dimethyldithiocarbamate Inhibit Ubiquitin Activation through Intracellular Metal Transport and Increased Oxidative Stress in HEK293 Cells. Chemical Research in Toxicology, 28(4), 682-690.
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4

2D DIGE Protein Identification Workflow

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2D DIGE (two-dimensional difference gel electrophoresis) and mass spectrometry protein identification were run by Applied Biomics (www.appliedbiomics.com). Briefly, image scans were performed immediately following the SDS-PAGE with Typhoon TRIO (GE Healthcare) by the protocols provided. The scanned images were then analyzed by Image QuantTL software (GE-Healthcare) and subjected to in gel analysis and cross-gel analysis using DeCyder software version 6.5 (GE-Healthcare). The ratio of protein differential expression was obtained from in gel DeCyder software analysis. The selected spots were picked by Ettan Spot Picker (GE-Healthcare) following the DeCyder software analysis and spot picking design. The selected protein spots were subjected to in-gel trypsin digestion, peptide extraction, desalting and followed by MALDI-TOF/TOF.
Lin Z., Roche M.E., Díaz-Barros V., Domingo-Vidal M., Whitaker-Menezes D., Tuluc M., Uppal G., Caro J., Curry J.M, & Martinez-Outschoorn U. (2024). MiR-200c reprograms fibroblasts to recapitulate the phenotype of CAFs in breast cancer progression. Cell Stress, 8, 1-20.
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5

Proteomics Analysis of Extracted Proteins

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Total proteins were extracted and purified from fresh tissues using a ReadyPrep™ Protein Extraction kit (GE Healthcare Bio-science, Fairfield, CT, USA) following the procedure recommended by the manufacturer. A 2-D Quant Kit (GE Healthcare Bio-science) was used to determine the concentrations of total proteins. Proteomics analysis was performed as previously described11 (link). Protein samples were separated by 2-DE. The 20-cm IPG strips (pH 3–10) were loaded with samples and subjected to rehydration overnight. Samples containing 150 μg of protein for analytical gels and unlabeled samples containing 1 mg of protein were diluted to 450 μl with a rehydration solution and used for isoelectric focusing (IEF). After SDS-PAGE, each gel was stained with Coomassie brilliant blue dye and scanned with UMAXpowerlook 1120 (UMAX, Taipei, Taiwan). The DeCyder software version 6.5 (GE) was used to spot detect and determine quantity, intergel matching, and statistics. The statistical significance was assessed for each change in abundance using a one-way ANOVA. We selected protein spots for which the mean ratio was greater than 1.5-fold or less than −1.5-fold.
Wu P., Quan H., Kang J., He J., Luo S., Xie C., Xu J., Tang Y, & Zhao S. (2017). Downregulation of Calcium-Binding Protein S100A9 Inhibits Hypopharyngeal Cancer Cell Proliferation and Invasion Ability Through Inactivation of NF-κB Signaling. Oncology Research, 25(9), 1479-1488.
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6

Protein Differential Expression Analysis

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Image scans were carried out immediately following the SDS/PAGE using Typhoon TRIO (GE Healthcare) following the manufacturer’s protocols. The scanned images were analyzed by Image QuantTL software (GE Healthcare), and then, in‐gel analysis and cross‐gel analysis was performed using DeCyder software version 6.5 (GE Healthcare). The ratio change of the protein differential expression was obtained from in‐gel DeCyder software analysis.
Huang H., Dabrazhynetskaya A., Pluznik J., Zheng J., Wu Y., Chizhikov V., Buehler P.W., Yamada K.M, & Dhawan S. (2021). Hemin activation abrogates Mycoplasma hyorhinis replication in chronically infected prostate cancer cells via heme oxygenase‐1 induction. FEBS Open Bio, 11(10), 2727-2739.
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7

Phosphoproteomic Analysis by 2D-DIGE

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Phosphoprotein analysis was performed using 2-D DIGE using CyDye staining and MALDI-MS for identification as previously described [22] . Image scans were carried out immediately following the SDS-PAGE using Typhoon TRIO (Amersham BioSciences) following the protocols provided. The scanned images were analyzed by Image QuantTL software (GE-Healthcare), and then subjected to in-gel analysis and cross-gel analysis using DeCyder software version 6.5 (GE-Healthcare). The ratio change of the protein differential expression was obtained from in-gel DeCyder software analysis.
Kotlo K., Xing Y., Lather S., Grillon J.M., Johnson K., Skidgel R.A., Solaro R.J, & Danziger R.S. (2014). PR65A Phosphorylation Regulates PP2A Complex Signaling. PLoS ONE, 9(1), e85000.
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