We utilized LabScan image scanner (version 5; Amersham, Germany) to capture and store the 2-DE gel images. PD-Quest™ 2-D gel analysis software (Version 8.0.1, Bio-Rad) was used to detect, match, and quantify the distinct protein spots. In order to identify differentially expressed serum proteins, the percentages of volume contributions (vol%) were calculated (i.e., the spot volume of a specific protein as a percentage of the total spot volume of all proteins in the gel, including unresolved peptides).
Pdquest 2d gel analysis software
Manufactured by Bio-Rad
Sourced in Germany
PDQuest 2D Gel Analysis software is a computer program designed for the analysis of two-dimensional (2D) gel electrophoresis data. It provides tools for image acquisition, spot detection, and quantitative analysis of protein expression levels.
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Lab products found in correlation
6 protocols using pdquest 2d gel analysis software
1
Serum Proteome Analysis Using 2-DE
2
2-DE Gel Image Analysis Protocol
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The ImageScanner III (GE Healthcare, Sweden) was used to capture and store 2-DE gel images. PD-Quest 2-D gel analysis software (version 8.0.1, Bio-Rad) was employed to evaluate the differentially expressed protein spots. Identical spots were matched in the serial gels and normalized by correcting for spot quantification values and gel-to-gel variation unrelated to expression changes. For the normalization method, we used total densities from the gel images (i.e., raw quantity of each gel spot was divided by the total quantity of all spots within the gel). All protein concentration values are presented as means of percentage volume (% volume) ± standard deviations (SD). The student’s t-test and one-way analysis of variance (ANOVA) were used to analyze differences between patients and controls. P-values less than 0.05 (p<0.05) were considered as statistically significant.
3
2D Gel Analysis for Protein Profiling
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The gels were scanned with gel imager (GS-800, Bio-Rad). Three biological replicates of 2D gel had a correlation coefficient value above 0.65. For each protein sample, spots were detected and matched automatically and edited manually with PDQuest 2D gel analysis software (version 8.1.0, Bio-Rad). The detected spots presented in all the replicate gels to be accounted. Student’s t-test was used to determine statistically significance (P < 0.05).
4
2D Gel Electrophoresis Protein Quantification
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Images of silver-stained 2D-E gels were captured using a LabScan scanner (version 5; Amersham, Germany), and PD-Quest™ 2D gel analysis software (version 8.0.1, Bio-Rad) was used to detect, match, and quantify protein spots. Normalization was achieved by dividing the raw quantity of each spot in the gel by the total intensity of pixels in the image in order to compensate for non-expression related variations in protein spot intensities. The variance ratio test (F) was used to analyse differences among the sample groups. A p-value less than 0.05 was considered statistically significant.
5
Two-Dimensional Protein Separation Protocol
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Two-dimensional separation of tested protein isolates was run using a commercial Ready Prep 2D Starter Kit (Bio Rad) following the manufacturer's protocol. Upon completion of the separation, the gels were stained overnight with a staining buffer. They were destained with a destaining buffer for 3 h. The gels were documented using a gel documentation system and analyzed with the PDQuest 2D Gel Analysis software (Bio-Rad).
6
Bacterial Adhesion Proteome Analysis
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Gels containing extracellular proteins from the tested bacterial strains were compared qualitatively and quantitatively in reference to bacterial adhesion to the epithelium using the PDQuest 2D Gel Analysis software (Bio-Rad). Ten spots differentiating weakly and strongly adherent strains were selected. Spots were cut and sent for analysis at the Mass Spectrometry Laboratory, the Institute of Biochemistry and Biophysics PAS in Warsaw to be analyzed using LC-ESI-MS/MS tandem mass spectrometry.
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