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There is apparently room for improvement in scoring spectrum with little information.
Only proteins with at least two different identified peptides with significantly scored spectra, which passed manual verification were considered.
The resulting scored spectra have more intensity assigned to true fragment masses and feature a much smaller number of noise peaks while simultaneously retaining almost all b/ y-ions.
On the basis of the above observations, we sought to determine if it was possible to associate each factor score spectrum to real wound bed constituents that are typically present during the course of healing.
We saw this problem for example in item 7. When all children between 0 7 years were included, untreated, treated and relapsing feet were assessed which meant that the whole scoring spectrum was used.
The observed retention time of each confident peptide was assigned by first considering the best scoring spectrum for that particular peptide, and then use Bullseye version 1.30 to find for each such spectrum the apex retention time of its corresponding feature.
We had looked into a large number of score histograms from scoring various spectra, and all of them show excellent theoretical fits.
We verified this prediction by obtaining a high degree of fit between each factor score spectrum and spectra obtained from pure wound bed constituents using non-negative least-squares fitting (results described further below).
For the NNLS analysis, R (coefficient of multiple correlation) > 0.9 for all factor score spectra.
Factor scores were also normalized and scaled to convert them into "factor score spectra" which were fitted with real spectra belonging to the 7 different wound bed constituents using Non-Negative Least Squares (NNLS) analysis using MATLAB (v. R2012b) to correlate the factor score spectra with spectra of the 7 pure wound bed constituents.
Multivariate factor analysis was performed on all spectra representing individual wounds using XLSTAT version 2013.1.02 (MS Excel add-in) to express the spectra as a weighted sum of 3 "factor score spectra" with the weights termed as "factor loadings".
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