PXD029039

PXD029039 is an original dataset announced via ProteomeXchange.

Title	Well-plate uFASP for proteomic analysis of single pancreatic islets
Description	Filter-aided sample preparation (FASP) is widely used in bottom-up proteomics for tryptic digestion. However, the sample recovery yield of this method is limited by the amount of starting material. While ~100 ng of digested protein sample is sufficient for thorough protein identification, proteomic information gets lost after digestion of samples with a protein content < 10 µg due to incomplete peptide recovery from the filter. By reducing the filter area as well as the volumes of all reagents, we developed and optimized a well-plate µFASP device and protocol that is suitable for ~1 µg protein sample. In 1 µg of HeLa digest, we identified 1295 ± 10 proteins with our method followed by analysis with liquid chromatography–mass spectrometry. In contrast, only 524 ± 5 proteins were identified with the standard FASP protocol while 1395 ± 4 proteins were identified in 20 µg after standard FASP as a benchmark. Furthermore, we used our method to conduct a combined peptidomic and proteo-mic study of single islets of Langerhans. Here, we separated neuropeptides from single islets as effluents from a ⌀ 1 mm molecular cut-off filter and digested the remaining on-filter proteins for bottom-up proteomic analysis. Our results indicate inter-islet heterogeneity for expression of proteins involved in glucose catabolism, pancreatic hormone processing and secreted peptide hormones. We consider our method to provide a useful tool for proteomic characterization of samples where biological material is scarce.
HostingRepository	PRIDE
AnnounceDate	2022-04-13
AnnouncementXML	Submission_2022-04-13_03:30:40.931.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD029039
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Erik Jansson
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	amidated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2021-10-10 23:25:03	ID requested
⏵ 1	2022-04-13 03:30:41	announced

submitter keyword: FASP, islets of Langerhans, method development

Erik Jansson
contact affiliation	Department of Pharmaceutical Biosciences, Uppsala University
contact email	erik.jansson@farmbio.uu.se
lab head
Erik Jansson
contact affiliation	Uppsala University
contact email	erik.jansson@farmbio.uu.se
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/2022/04/PXD029039

PRIDE project URI

• PRIDE
  1. PXD029039
     1. Label: PRIDE project
     2. Name: Well-plate uFASP for proteomic analysis of single pancreatic islets