Bio Tool Kit microapp cannot manually sequence peptide MS/MS data from EAD-derived fragments

For research use only. Not for use in diagnostic procedures.

Answer

The Bio Tool Kit microapp embedded in PeakView® or SCIEX OS Software cannot perform de novo manual sequencing of peptides or MS/MS fragment matching for peptides fragmented using electron activated dissociation (EAD) from a ZenoTOF 7600 system. The MS/MS data obtained by EAD is too complex and fragment-rich, presenting the software with too many options for potential fragment ions; however, the Bio Tool Kit app can process MS/MS data acquired by CID (collision-induced dissociation). These EAD-based MS/MS spectra can be automatically interpreted and annotated by Biologics Explorer software if the sequences are already known. To process de novo sequencing data, software from third-party vendors, such as Peaks software, is required.

For peptide MS/MS data acquired by CID, users can follow three steps to perform de novo sequencing using Bio Tool Kit: 

1. Highlight a fragment ion as a starting point for manual sequencing.
2. Double-click on the caption for the peak to characterize it.
3. View the peptide sequence ladder to obtain the final results.

Analysis of peptide fragment MS/MS spectra using Bio Tool Kit has been described elsewhere:
1) In this article: https://sciex.com/support/knowledge-base-articles/how-to-use-bio-tool-kit-for-interpreting-peptide-ms-ms-data-acquired-with-cid-and-ead-fragmentation_en_us
2) In this SCIEX community post: https://community.sciex.com/2021/08/07/using-bio-tool-kit-for-interpreting-peptide-ms-ms-data-obtained-using-electron-activated-dissociation-ead/