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PXD021489

PXD021489 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleBAC-DROP: Rapid digestion of proteome fractionated via dissolvable polyacrylamide gel electrophoresis and its application to bottom-up proteomics workflow
DescriptionThe GeLC-MS workflow, which combines low-cost, easy-to-use SDS-polyacrylamide gel electrophoresis (SDS-PAGE) with liquid chromatography-mass spectrometry (LC-MS), is very popular in current bottom-up proteomics. However, GeLC-MS requires that PAGE-separated proteins undergo overnight enzymatic digestion in a gel, resulting in more than 20 hours of sample preparation for LC-MS. In this study, we overcame the limitations of GeLC-MS by developing a rapid digestion workflow for PAGE separation proteins using N,N'-bis(acryloyl)cystamine (BAC) cross-linked gels that can be solubilized by reductive treatment. Making use of an established workflow called BAC-DROP (BAC-gel dissolution to digest PAGE-resolved objective proteins), crude proteome samples were fractionated based on molecular weight by BAC cross-linked PAGE. After fractionation, the gel fragments were reductively dissolved in under 5 minutes, and in-solution trypsin digestion of the protein released from the gel was completed in less than 1 hour at 70 °C, equivalent to a 90–95 % reduction in time compared to conventional in-gel trypsin digestion. The introduction of the BAC-DROP workflow to the MS assays for inflammatory biomarker CRP and viral marker HBsAg allowed for serum sample preparation to be completed in as little as 5 hours, demonstrating successful marker quantification from a 0.5 μL sample of human serum. Combining reduced proteome complexity via PAGE fractionation with rapid trypsin digestion provides a unique opportunity for conducting high-throughput analysis of in-depth proteome with a focus on specific molecular weight ranges.
HostingRepositoryPanoramaPublic
AnnounceDate2021-01-24
AnnouncementXMLSubmission_2021-01-24_19:42:51.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterNobuaki Takemori
SpeciesList scientific name: Homo sapiens; NCBI TaxID: 9606; scientific name: Bos taurus; NCBI TaxID: 9913; scientific name: Hepatitis B virus; NCBI TaxID: 10407;
ModificationListLabel:13C(6)15N(2); Label:13C(6)15N(4)
InstrumentQTRAP 5500
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-09-15 05:46:34ID requested
12020-12-25 13:13:20announced
22021-01-24 19:42:52announced: Added PubMed ID
Publication List
Takemori A, Ishizaki J, Nakashima K, Shibata T, Kato H, Kodera Y, Suzuki T, Hasegawa H, Takemori N, BAC-DROP: Rapid Digestion of Proteome Fractionated via Dissolvable Polyacrylamide Gel Electrophoresis and Its Application to Bottom-Up Proteomics Workflow. J Proteome Res, ():(2020) [pubmed]
Keyword List
submitter keyword: BAC-PAGE, Bottom-up proteomics, Dissolvable polyacrylamide gel, GeLC-MS, Rapid enzymatic digestion
Contact List
Nobuaki Takemori
contact affiliationEhime University
contact emailtakemori@m.ehime-u.ac.jp
lab head
Nobuaki Takemori
contact affiliationEhime University
contact emailtakemori@m.ehime-u.ac.jp
dataset submitter
Full Dataset Link List
Panorama Public dataset URI