Proteomics

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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

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Publications

Comprehensive de Novo Peptide Sequencing from MS/MS Pairs Generated through Complementary Collision Induced Dissociation and 351 nm Ultraviolet Photodissociation.

Horton Andrew P AP   Robotham Scott A SA   Cannon Joe R JR   Holden Dustin D DD   Marcotte Edward M EM   Brodbelt Jennifer S JS  

Analytical chemistry 20170308 6

We describe a strategy for de novo peptide sequencing based on matched pairs of tandem mass spectra (MS/MS) obtained by collision induced dissociation (CID) and 351 nm ultraviolet photodissociation (UVPD). Each precursor ion is isolated twice with the mass spectrometer switching between CID and UVPD activation modes to obtain a complementary MS/MS pair. To interpret these paired spectra, we modified the UVnovo de novo sequencing software to automatically learn from and interpret fragmentation sp  ...[more]

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