Preprocessing DIA data

1 Preprocessing DIA data

2 Questions for Dr. Edwards

1. What is the best way to document method(s) used to make the spectral libraries?

1. Are there best ways to document the initial spectral search? (eg. parameters used which I have either not noticed or paid proper attention to in other publications.

2. What are the most relevant metrics to collect while generating the spectral libraries?

1. How best to present them?

3. Cost/Benefit of HCD/CID DDA runs for the spectral libraries?
4. Given the following possible metrics of my spectral consensus, are there best ones to examine for problems in the library? :

1. PrecursorMz ProductMz Tr_recalibrated transition_name CE LibraryIntensity transition_group_id decoy PeptideSequence ProteinName Annotation FullUniModPeptideName PrecursorCharge PeptideGroupLabel UniprotID FragmentType FragmentCharge FragmentSeriesNumber LabelType

5. Favorite window sizes?
6. When is it appropriate to use the ‘OpenSwathWorkflow’ vs. invoking the various parts of it separately? How does one evaluate this?
7. What metrics from the swath search are the most appropriate to report/plot/examine?
8. There are >= 2 methods for feature alignment following the swath search. How does one choose the appropriate method (so far I chose the shortest method).
9. Given the similarity of the final, feature-aligned data to an RNASeq expressionset, what is the cost/benefit of recasting it into one?