PXD006038

PXD006038 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Complementary CID and 351 nm UVPD tandem mass spectra enable effective de novo sequencing
Description	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.
HostingRepository	MassIVE
AnnounceDate	2017-03-06
AnnouncementXML	Submission_2017-03-06_22:26:13.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andrew Horton
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	unknown modification: [N-term] [215.058243] AMCA; Carbamyl; Oxidation
Instrument	instrument model: Thermo Scientific Velos Pro mass spectrometer modified to enable 351 nm UVPD

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2017-03-06 18:18:31	ID requested
⏵ 1	2017-03-06 22:26:14	announced

Publication List

Horton AP, Robotham SA, Cannon JR, Holden DD, Marcotte EM, Brodbelt JS, Comprehensive de Novo Peptide Sequencing from MS/MS Pairs Generated through Complementary Collision Induced Dissociation and 351 nm Ultraviolet Photodissociation. Anal Chem, 89(6):3747-3753(2017) [pubmed]

Horton AP, Robotham SA, Cannon JR, Holden DD, Marcotte EM, Brodbelt JS, Comprehensive de Novo Peptide Sequencing from MS/MS Pairs Generated through Complementary Collision Induced Dissociation and 351 nm Ultraviolet Photodissociation. Anal Chem, 89(6):3747-3753(2017) [pubmed]

Keyword List

submitter keyword: 351 nm UVPD, ultraviolet photodissociation, AMCA, de novo

submitter keyword: 351 nm UVPD, ultraviolet photodissociation, AMCA, de novo

Contact List

principal_investigator
lab head
Andrew Horton
contact affiliation	UT Austin
contact email	ahorton@utexas.edu
dataset submitter

Full Dataset Link List

MassIVE dataset URI
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MassIVE dataset URI

Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive.ucsd.edu/MSV000080603