PXD027521 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-07-23 08:03:59 | ID requested | |
⏵ 1 | 2021-11-15 08:13:58 | announced | |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: synthetic biology, QconCAT, quantitative proteomics, loop assembly |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD027521
- Label: PRIDE project
- Name: Synthetic biology meets proteomics: Construction of à la carte QconCATs for absolute protein quantification C4PR_LIV