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Mascot generic format (mgfs) files were generated from MS and MS/MS raw data.
Then, a total of 83,242 scaffold files were generated from the collected 243,130 natural products in the NPDB.
To visualize the reads along the fission yeast genome, wiggle files were generated from uniquely mapped reads based on their location and counts.
To identify peptides, data files were generated from the MS/MS scans by Bioworks 3.0 using the SEQUEST algorithm (threshold, 105; minimum group scan 2, Xc >1.0, Thermo Fisher Scientific) and searched against the complete amino acid database derived from the B. pertussis Tohama genome database.
Four files were generated from each dataset and the mean value was computed.
STS files were generated from a Filemaker Pro database using the Troi File Plug-in 32.
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To view the data and result in IGB browser (HTTP://igb.bioviz.org), SGR files are generated from BAF and LRR, and WIG files are generated from copy number and allelic imbalance.
BigBed files are generated from Browser Extensible Data (BED) files.
Such relationships include both sample information for example, that two files are generated from the same or related biological samples and process information or provenance for example, that a result file was generated by using a specific program and auxiliary data to analyse a set of data files.
A MASCOT generic file was generated from all exported MS/MS spectra from Progenesis software.
The first set of reference data (i.e., treatment A) corresponds to a batch of nA = 65 CEL files obtained from GEO, where each CEL file was generated from an array hybridization with source material isolated from mouse liver (Table S1).The second set of reference data (i.e., treatment B) corresponds to a batch of nB CEL files from the jth leukocyte population (Table S2).
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