PXD003403

PXD003403 is an original dataset announced via ProteomeXchange.

Title	Denaturing and native top-down venomics: Mapping proteoforms and protein complexes from king cobra venom
Description	Characterizing whole proteins by top-down proteomics avoids a step of inference encountered in the dominant bottom-up methodology when peptides are assembled computationally into proteins for identification. The direct interrogation of whole proteins and protein complexes from the venom of Ophiophagus hannah (king cobra) provides a sharply clarified view of toxin sequence variation, transit peptide cleavage sites and post-translational modifications (PTMs) likely critical for venom lethality. A tube-gel format for electrophoresis (called GELFrEE) and solution isoelectric focusing were used for protein fractionation prior to LC-MS/MS analysis resulting in 131 protein identifications (18 more than bottom-up) and a total of 184 proteoforms characterized from 14 protein toxin families. Operating both GELFrEE and mass spectrometry to preserve non-covalent interactions generated detailed information about two of the largest venom glycoprotein complexes: the homodimeric L-amino acid oxidase (LAAO, ~130 kDa) and the multi-chain toxin cobra venom factor (~147 kDa). The LAAO complex exhibited two clusters of multi-proteoform complexes corresponding to the presence of 5 or 6 N-glycans moieties, each consistent with a distribution of N-acetyl hexosamines. Employing top-down proteomics in both native and denaturing modes provides unprecedented characterization of venom proteoforms and their complexes. A precise molecular inventory of venom proteins will propel the study of snake toxin variation and the targeted development of new anti-venoms or other biotherapeutics.
HostingRepository	PRIDE
AnnounceDate	2016-05-18
AnnouncementXML	Submission_2016-05-18_02:28:45.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	RAFAEL MELANI
SpeciesList	scientific name: Ophiophagus hannah (King cobra) (Naja hannah); NCBI TaxID: 8665;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2016-01-04 06:38:54	ID requested
⏵ 1	2016-05-18 02:28:46	announced

Melani RD, Skinner OS, Fornelli L, Domont GB, Compton PD, Kelleher NL, Mapping Proteoforms and Protein Complexes From King Cobra Venom Using Both Denaturing and Native Top-down Proteomics. Mol Cell Proteomics, 15(7):2423-34(2016) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: King cobra venom, top-down proteomics, proteoforms, protein complexes, native mass spectrometry

Gilberto B Domont
contact affiliation	Institute of Chemistry, Universidade Federal do Rio de Janeiro Av Athos da Silveira Ramos, 149, CT- A-542, Cidade Universitária 21941-909 Rio de Janeiro, RJ Brazil
contact email	gilberto@iq.ufrj.br
lab head
RAFAEL MELANI
contact affiliation	Universidade Federal do Rio de Janeiro
contact email	Melanirafael@yahoo.com.br
dataset submitter

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://ftp.pride.ebi.ac.uk/pride/data/archive/2016/05/PXD003403

PRIDE project URI

• PRIDE
  1. PXD003403
     1. Label: PRIDE project
     2. Name: Denaturing and native top-down venomics: Mapping proteoforms and protein complexes from king cobra venom