Supplementary Figure 2: Details on data reduction in the data analysis workflow. | Nature Methods

Supplementary Figure 2: Details on data reduction in the data analysis workflow.

From: Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins

Supplementary Figure 2

The sample data is submitted into the ID filter pipeline. Here, a search is performed against the target-decoy version of a protein database containing the proteome of the species of interest as well as contaminant sequences. Peptides below a certain false discovery rate (FDR; default 1%) are considered as good matches and reported in an idXML file. Corresponding MS/MS spectra are removed from the mzML file. Next, the RNPxlXICFilter tool automatically screens whether the precursors of remaining MS/MS spectra also appear in the non-irradiated control. To this end, extracted ion chromatograms of those precursors are calculated in UV and control sample. MS/MS spectra of precursors appearing in both samples with comparable intensities, i.e. less than double in the UV sample, are not written into the output mzML file.

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