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Figure 2 | BMC Bioinformatics

Figure 2

From: PPINGUIN: Peptide Profiling Guided Identification of Proteins improves quantitation of iTRAQ ratios

Figure 2

Workflow. Standard workflow of proteomics data evaluation (left hand side) compared to the PPINGUIN workflow presented in our manuscript (right hand side). Starting point for both workflows is the mzML [48] file containing the spectral peak data. In contrast to the standard workflow we employ clustering as a very early step prior to protein inference. This leads to splitting of spectra into different groups. Quantitation and identification is performed independently for each group. The result is a list of identified and quantified proteins ready for downstream analysis.

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