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Spectra were analyzed and peak list for apo and ligand bound samples were generated using NMRView [36].
A core set of peaks shared by all eleven programs was identified and found to comprise 75 80% of the smallest peak list for each ChIP-seq dataset (Figure 3).
ChIP-seq peak list for USF1.
The peak list for the search was generated by Xcalibur 1.3.
On-the-fly alignment was used with quality control samples manually selected as the peak list for primary alignment.
In addition, users can obtain the peak list for each spectrum, the corresponding identified or unidentified compounds and their concentrations.
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Peak lists for database searching were created using Mascot Distiller (Version 1; MatrixScience, London, UK).
ProteinLynx Global Server software (V2.2.5) was used to convert raw data to peak lists for database searching.
Peak lists for the database search were produced in the Mascot generic format using BioWorks 3.3.1 (Thermo Finnigan, San Jose, CA) and DTASuperCharge V 1.31 (SourceForge), and the derived peak lists were searched using the Mascot 2.2.04 search engine (Matrix Science, London, UK) against a real and false IPI human database (V3.56, including 153, 078 protein entries).
The raw data for each run were first extracted to provide MS/MS peak lists for identification- and intensity-based profile peak lists for quantification.
The GMD [ 26] provides public access to GC-MS data and peak lists for plant metabolites.
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