Complementary CID and 351 nm UVPD tandem mass spectra enable effective de novo sequencing

ABSTRACT: This dataset accompanies a publication in which we present a strategy for acquisition and effective de novo peptide sequencing of complementary CID and 351 nm ultraviolet photodissociation (UVPD) MS/MS pairs. E. coli whole cell lysate is carbamylated to block lysine side chains, digested with trypsin (now active only at Arg residues), and N-terminally tagged with the chromophore AMCA. Three technical replicates were analyzed using a Thermo Velos Pro dual linear ion trap mass spectrometer coupled to a Coherent 351 nm excimer laser. Each precursor ion is isolated twice with the mass spectrometer switching between CID and UVPD activation modes to obtain a complementary MS/MS pair. We modified our UVnovo de novo sequencing software to automatically learn from and interpret fragmentation spectra from any combination of complementary activation methods, and we used this to analyze the CID/UVPD paired spectra. This performance exceeds that of PEAKS and PepNovo on the CID spectra alone and demonstrates that CID/UPVD brings significant advantages for comprehensive and accurate de novo peptide sequencing.

INSTRUMENT(S): Thermo Scientific Velos Pro mass spectrometer modified to enable 351 nm UVPD

ORGANISM(S): Escherichia Coli (ncbitaxon:562)

SUBMITTER: Jennifer Brodbelt   Edward Marcotte  

PROVIDER: MSV000080603 | MassIVE | Mon Mar 06 18:18:00 GMT 2017

SECONDARY ACCESSION(S): PXD006038

REPOSITORIES: MassIVE