PXD009800

PXD009800 is an original dataset announced via ProteomeXchange.

Title	Multi-Enzymatic Limited Digestion - the Next-Generation Sequencing for Proteomics
Description	An innovative approach merging both the bottom-up and middle-down ideologies to provide fast, robust and comprehensive solutions for proteomics studies. The methodology, referred to as MELD for Multiple-Enzymatic Limited Digestion, capitalizes on a single two-hour long proteolytic step involving the synergic action of a diluted mix of several enzymes. While the multi-enzymatic benefits are retained, the lower enzyme concentrations induce a limitation in the proteolytic reaction. This feature engenders numerous missed cleavage events and results in abundant peptides of diverse length with overlapping stretches of residues. This outcome eventually increases the extent and confidence in the sequence coverage while opening roads for refined and comprehensive protein characterization. We here use Adalimumab, a therapeutic ~144 kDa human immunoglobulin G IgG1 as a candidate molecule to compare the respective efficacy of state-of-the-art complete mono-enzymatic strategies encompassed in individual or combinational workflows with the standard MELD protocol for extensive protein characterization. The benchmarking analysis was performed over 12 Adalimumab samples issued from independent proteolytic digestions: 6 samples were processed using the MELD methodology, 3 with the combinatory methodology and 3 with the mono-enzymatic tryptic methodology. They were all subjected to independent database searches, using both constrained and unconstrained cleavage site rules for the latter.
HostingRepository	PRIDE
AnnounceDate	2019-05-08
AnnouncementXML	Submission_2019-05-08_08:57:59.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Gabriel Mazzucchelli
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; complex glycosylation; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-05-16 06:24:17	ID requested
⏵ 1	2019-05-08 08:58:01	announced

Morsa D, Baiwir D, La Rocca R, Zimmerman TA, Hanozin E, Grifn, é, e E, Longuesp, é, e R, Meuwis MA, Smargiasso N, Pauw E, Mazzucchelli G, Multi-Enzymatic Limited Digestion: The Next-Generation Sequencing for Proteomics? J Proteome Res, 18(6):2501-2513(2019) [pubmed]

curator keyword: Technical

submitter keyword: Proteolytic method, Limited digestion, Protein characterization, PTMs, de novo sequencing

mAbs, Digestibility profile, Mass spectrometry

Gabriel Mazzucchelli
contact affiliation	Laboratory of Mass Spectrometry-MolSys, Department of Chemistry, University of Liege, Liege, Belgium.
contact email	gabriel.mazzucchelli@uliege.be
lab head
Gabriel Mazzucchelli
contact affiliation	Mass Spectrometry Laboratory
contact email	gabriel.mazzucchelli@uliege.be
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/2019/05/PXD009800

PRIDE project URI

• PRIDE
  1. PXD009800
     1. Label: PRIDE project
     2. Name: Multi-Enzymatic Limited Digestion - the Next-Generation Sequencing for Proteomics