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Figure 1 | Journal of Clinical Bioinformatics

Figure 1

From: Availability of MudPIT data for classification of biological samples

Figure 1

MudPIT workflow. Enzymatic digested peptides are first separated by Strong Cation Exchange (SCX), using steps of increasing salt concentration, followed by Reverse Phase (RP) chromatography, using an acetonitrile gradient. Eluted peptides are then directly analyzed by tandem mass spectrometry producing MS and MS/MS spectra. By specific algorithm, such as SEQUEST, and applying appropriate criteria of data filtering (see Additional file 2), the comparison of experimental MS and MS/MS spectra with those in-silico predicted from a protein sequence database allows the characterization of the peptide sequences and the corresponding proteins, without limits of isoelectric point (pI), molecular weight (Mw) or hydrophobicity. Using MudPIT, five different datasets per sample were collected for the study purposes. Specifically, in addition to complete protein and peptide profiles, m/z data, corresponding to 60 mM, 120 mM, 400 mM of salt concentration steps, were mined collecting three different datasets of spectra.

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