PXD006835

PXD006835 is an original dataset announced via ProteomeXchange.

Title	Direct identification of functional amyloid proteins in cell lysate by label-free quantitative mass spectrometry
Description	Functional amyloids are important structural and functional components in many biofilm, yet our knowledge of these fascinating polymers is limited to a few examples for which the amyloid have been purified and characterized by mass spectrometry. Isolation of the functional amyloid from other cell components represents the major bottleneck in the identification of novel functional amyloids. Here we present a label-free quantitative mass spectrometry based method that allows identification of amyloid proteins directly in cell lysates treated with increasing concentrations of formic acid (0-100%). Many functional amyloids are only depolymerized in the presence of concentrated formic acid and provide a characteristic sigmoidal signature when protein abundance is plotted against the formic acid concentration. An automated data processing pipeline was developed to provide a shortlist of amyloid protein candidates based on the amyloid specific abundance signature. The method was evaluated using the E. coli curli and the Pseudomonas Fap system. The major amyloid subunit was confidently identified for both systems and the minor subunit was also identified for the curli system. In addition, very few false positive candidates were identified and these could easily be discarded bases on bioinformatics analysis. Finally, we provide evidence for the application of the method for complex samples with low diversity. This provides an opportunity to identify amyloid in e.g. clinical biofilms.
HostingRepository	PRIDE
AnnounceDate	2017-08-09
AnnouncementXML	Submission_2017-08-09_01:31:46.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Florian-Alexander Herbst
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Pseudomonas sp. UK4; NCBI TaxID: 452680;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-06-29 23:26:46	ID requested
⏵ 1	2017-08-09 01:31:47	announced

Danielsen HN, Hansen SH, Herbst FA, Kjeldal H, Stensballe A, Nielsen PH, Dueholm MS, Direct Identification of Functional Amyloid Proteins by Label-Free Quantitative Mass Spectrometry. Biomolecules, 7(3):(2017) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: functional amyloids, biofilm, nanomaterials, mass spectrometry

Per Halkjær Nielsen
contact affiliation	Aalborg University Fredrik Bajers Vej 7H 9220 Aalborg Denmark
contact email	phn@bio.aau.dk
lab head
Florian-Alexander Herbst
contact affiliation	Aalborg University
contact email	fah@bio.aau.dk
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/2017/08/PXD006835

PRIDE project URI

• PRIDE
  1. PXD006835
     1. Label: PRIDE project
     2. Name: Direct identification of functional amyloid proteins in cell lysate by label-free quantitative mass spectrometry