Dear TPP users, I seek to construct a SpectraST spectral library to interrogate SWATH datasets.
To construct such a library, I search high-accuracy TripleTOF IDA datasets using TANDEM, with 50 ppm as the +- parent errors and 100 ppm as the fragment error. Searching the decoy database using the "scoring, include reverse" TANDEM parameter, or decoyFastaGenerator-made decoys produces a very small number of IDs relative to the target sequences. For instance, with the +decoy search, I obtain 9424 assigned / 3650 unique / 65 decoy matches; with the -decoy search, I obtain 9390 assigned / 3637 unique.Here, 'maximum valid expectation value' set to 1e-2 for both 'output' and 'refine' TANDEM parameters. Broadening the parent and fragment windows (to 200 ppm, for instance) does not significantly increase the number of hits against the decoy dataset. It is my understanding that the peptideProphet and interProphet classifiers depend on well-resolved and populous distributions of true and false-positive IDs in order to build a useful discriminant. It seems that these methods would break down given significantly fewer data for FP or TP hits. I believe that SpectraST expects iProphet spectral probabilities / expectation values in order to aggregate experimental spectra. Can you suggest a method to accurately estimate these probabilities given few decoy hist, instead of simply accepting all spectral identifications? Thank you! Vadim -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
