PXD003767

PXD003767 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	AMCA chromophore tagging and 351 nm ultraviolet photodissociation enables de novo sequencing of E. coli proteome
Description	Demonstration of novel experimental and computational pipeline for high performance de novo peptide sequencing. 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. 351 nm ultraviolet photodissociation (UVPD) of parent peptides produces MS2 spectra dominated by the y-type ion series. We developed the software tool UVnovo for de novo sequencing of these spectra and used Proteome Discoverer SEQUEST/Percolator to generate a dataset for training and validation. UVnovo results provided here derive from a 3-fold cross validation regime. Our methods and dataset are described in the accompanying publication.
HostingRepository	MassIVE
AnnounceDate	2016-03-10
AnnouncementXML	Submission_2016-03-10_19:43:49.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	2016-03-10 19:28:07	ID requested
⏵ 1	2016-03-10 19:43:52	announced

Publication List

Robotham SA, Horton AP, Cannon JR, Cotham VC, Marcotte EM, Brodbelt JS, UVnovo: A de Novo Sequencing Algorithm Using Single Series of Fragment Ions via Chromophore Tagging and 351 nm Ultraviolet Photodissociation Mass Spectrometry. Anal Chem, 88(7):3990-7(2016) [pubmed]

Robotham SA, Horton AP, Cannon JR, Cotham VC, Marcotte EM, Brodbelt JS, UVnovo: A de Novo Sequencing Algorithm Using Single Series of Fragment Ions via Chromophore Tagging and 351 nm Ultraviolet Photodissociation Mass Spectrometry. Anal Chem, 88(7):3990-7(2016) [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

Jennifer Brodbelt, Edward Marcotte
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/MSV000079571