GeneSpring MS Analytical Tool
GeneSpring MS Analytical Tool
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While microarray analysis is commonly associated with disease research and characterization, there are other experimental techniques being employed to identify critical biomarkers for early detection, enabling treatment before the disease progresses. Through combined liquid chromatography and mass spectrometry (LC/MS) applications, analysis of low molecular weight plasma fractions can lead to identification of biomarkers in cancer patients. Michael Holmes and colleagues performed comparative analysis of the low molecular weight fractions from pancreatic cancer and control plasma samples using LC/MS TOF to identify potential biomarkers. Mass Hunter software was used to detect and determine the abundance of features in each resulting chromatogram, and GeneSpring MS was used as an additional analytical tool. The group found that by using GeneSpring MS and cluster analysis options, they were able to identify 20 features that discriminated diabetic vs. non-diabetic pancreatic patients. This work provides important information on identifying and validating candidate biomarkers in future research.
Figure 1. Volcano plots of pancreatic samples in diabetics and non-diabetics.
Potential biomarkers are those with 2x higher or lower and with p-value < 0.05 and are denoted in red.
Figure 2. Cluster analysis of 445 features present in both diabetic and non-diabetics; the majority of features track in both diabetics and non-diabetics.
Genomic DNA of each individual S. aureus strain was labelled with Cy3 and co-hybridized with equivalent amounts of Cy5-labelled genomic DNA pooled from N315, Mu50 and COL. Background-subtracted data were expressed as Log10 ratios and analyzed by two-way clustering using GeneSpring 6.1. Probes yielding positive and negative signals are shown in blue and yellow, respectively. The significance of black bars (a, b, and c) is indicated in the text. Note that the figure resolution does not allow visualizing single probe differences but only clusters of probes.
Figure 3. The lower left panel from above showing 20 masses that are lower at least 2-fold different between control/cancer, decreased in diabetic cancer patients, and elevated in non-diabetic cancer patients.
View the Holmes et al poster featuring this data
GeneSpring MS: a comprehensive analytical tool for mass spectrometry that enables the rapid discovery of protein and metabolite biomarkers.
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For research use only and not for use in diagnostic procedures.