PXD027521

PXD027521 is an original dataset announced via ProteomeXchange.

Title	Synthetic biology meets proteomics: Construction of à la carte QconCATs for absolute protein quantification C4PR_LIV
Description	We report a new approach to the assembly and construction of QconCATs, quantitative concatamers for proteomic applications that yield stoichiometric quantities of sets of stable isotope-labelled internal standards. The new approach is based on synthetic biology precepts of biobricks, making use of loop assembly to construct larger entities from individual biobricks. It offers a major gain in flexibility of QconCAT implementation and enables rapid and efficient editability that permits, for example, substitution of one peptide for another. The basic building block (a Qbrick) is a segment of DNA that encodes two or more quantification peptides for a single protein, readily held in a repository as a library resource. These Qbricks are then assembled in a one tube ligation reaction that enforces the order of assembly, to yield short QconCATs that are useable for small quantification products. However, the DNA context of the short also allows a second cycle of assembly such that five different short QconCATs can be assembled into a longer QconCAT in a second, single tube ligation. From a library of Qbricks, a bespoke QconCAT can be assembled quickly and efficiently in a form suitable for expression and labelling in vivo or in vitro. We refer to this approach as the ALACAT strategy as it permits à la carte design of quantification standards.
HostingRepository	PRIDE
AnnounceDate	2021-11-15
AnnouncementXML	Submission_2021-11-15_08:13:57.841.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Catarina Franco
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-23 08:03:59	ID requested
⏵ 1	2021-11-15 08:13:58	announced

Dataset with its publication pending

submitter keyword: synthetic biology, QconCAT, quantitative proteomics, loop assembly

Robert J. Beynon
contact affiliation	Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Crown Street, L697ZB, Liverpool, United Kingdom
contact email	r.beynon@liverpool.ac.uk
lab head
Catarina Franco
contact affiliation	MRC Toxicology Unit University of Cambridge
contact email	cd735@cam.ac.uk
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/2021/11/PXD027521

PRIDE project URI

• PRIDE
  1. PXD027521
     1. Label: PRIDE project
     2. Name: Synthetic biology meets proteomics: Construction of à la carte QconCATs for absolute protein quantification C4PR_LIV