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Peak information from all acquired spectra was exported from the ProteinChip Software to SPSS 15.0 for statistical analysis.
To compare with dE2F1 and dE2F2 targets, peak information from dE2F1 and dE2F2 ChIP-chip in Drosophila melanogaster larvae (Korenjak et al. 2012) was annotated with HOMER.
Due to computation limitation, it is very slow to estimate all the peak information from a whole spectrum by proposed algorithm.
Data Explorer 4.5 (Applied Biosystems) and an in-house software package were used for the extraction of ion peak information from MS spectra.
Peak information from all fractions was combined together and analyzed using univariate statistics, as well as a linear, partial least squares discriminant analysis (PLS-DA), and a non-linear, random forest (RF), classification algorithm.
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2D H C and H N HSQC spectra of UDP-α d-[C,N]GlcNAc, Fc model showing the location of charged residues, representative line shapes and peak information extracted from 2D NMR measurements, and a H N HSQC-TROSY spectrum of (N-Y 2×[C,N]-GlcNAc -IgG1 N-Y 2×[C,N]-GlcNAc -IgG1
Peak information was downloaded from the Yale transcription factor binding site (TFBS) track of the ENCODE Project [ 80] with a preference for the assays from the HeLa-S3 cell line.
The sixth step reconstructs a high-resolution image from the peak information.
All data used to extract peak information, which was used to create the MS/MS peak list, were generated from one combined spectrum.
Some practitioners do analyze mixtures using quantitative peak information [10].
Peak information outputs were used for unsupervised biomarker clustering.
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