Answered Questions

Q: If a spliced peptide has multiple explanations as cis and/or trans, do you provide all these explanations or do you just report the sequence?

Spectra frequently have multiple possible cis- and trans- explanations. All cis-spliced peptide sequences are provided explanations from their parent protein(s) in the form of “ScanNumberIdentified_ProteinAccession_nStartResidue-nEndResidue_cStartResidue-cEndResidue | Proposed Cis Fusion Peptide”. Trans-spliced peptide sequences contain too many possible protein sources to realistically print, and as such are omitted in place of “ScanIdentified_Number”, where the Number is to provide a unique accession number when multiple spliced peptides match to the same spectrum. All cis-explanations are present in both the fasta and the results.

Q: There are some fasta files in the results with varying suffixes. What are these?

These fasta files are generated for some intermediate searches within the Neo-Fusion workflow. They contain an unfiltered list of all suspected spliced or nonspliced peptide sequences. The unfiltered nature of these intermediate databases (i.e. lots of incorrect sequences) makes them fairly useless for further downstream applications. They are written for diagnostic purposes only.

NC: cis-spliced sequences only. TS: trans-spliced sequences (No cis). All: cis- and trans-spliced sequences. TL: translated (normal/non-spliced/linear) peptides that, for whatever reason, were not identified in the traditional search. This typically is happens when conservative length parameters were chosen (e.g a user searches for peptides between 9-12 amino acids in length, but there’s an 8-mer or 13-mer peptide spectra).