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PXD019086-1

PXD019086 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleDeep learning the collisional cross sections of the peptide universe from a million experimental values
DescriptionThe size and shape of peptide ions in the gas phase are an under-explored dimension for mass spectrometry-based proteomics. To explore the nature and utility of the entire peptide collisional cross section (CCS) space, we measure more than a million data points from whole-proteome digests of five organisms with trapped ion mobility spectrometry (TIMS) and parallel accumulation – serial fragmentation (PASEF). The scale and precision (CV <1%) of our data is sufficient to train a recurrent neural network that accurately predicts CCS values solely based on the peptide sequence. Cross section predictions for the synthetic ProteomeTools library validate the model within a 1.3% median relative error (R > 0.99). Hydrophobicity, position of prolines and histidines are main determinants of the cross sections in addition to sequence-specific interactions. CCS values can now be predicted for any peptide and organism, forming a basis for advanced proteomics workflows that make full use of the additional information.
HostingRepositoryPRIDE
AnnounceDate2021-01-18
AnnouncementXMLSubmission_2021-01-18_08:49:43.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterMario Oroshi
SpeciesList scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Caenorhabditis elegans; NCBI TaxID: 6239; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932; scientific name: Drosophila melanogaster (Fruit fly); NCBI TaxID: 7227;
ModificationListNo PTMs are included in the dataset
InstrumenttimsTOF Pro
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-05-11 07:51:13ID requested
12021-01-18 08:49:44announced
22021-04-06 02:06:12announced2021-04-06: Updated publication reference for PubMed record(s): 33608539.
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: Technical, ion mobility, CCS, TIMS, deep learning
Contact List
Matthias Mann
contact affiliationDepartment Proteomics and Signal Transduction Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
contact emailmmann@biochem.mpg.de
lab head
Mario Oroshi
contact affiliationProteomics
contact emailoroshi@biochem.mpg.de
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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