TFExport is a tool that will export relevant information from peptides in a Skyline document for the purpose of importing directly into a Trace Finder compound database. Once a method has been optimized and finalized, information about each peptide (protein name, precursor m/z and z, product ion m/z and z, retention time, peak areas and ranking of product ions) is exported into a format that Trace Finder can read and use to process .raw files.
For best results, requirements include at least one data file with results for all peptides in the Skyline document. Product ions (“Targets”) can be exported individually and processed in parallel in Trace Finder, or one product ion per peptide (the most intense, by default) can be used for quantification and the remainder are used as confirming ions. Internal standards can be defined during the export process and analytes/internal standards can be linked once the file is imported into Trace Finder.