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

Sandbaumh, ü, ter FA, Nezhyva M, Eriksson O, Engberg A, Kreuger J, Andr, é, n PE, Jansson ET, FASP for Proteomic Analysis of Single Pancreatic Islets. J Proteome Res, 21(4):1167-1174(2022) [pubmed]

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

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PRIDE project URI

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