PXD053291
PXD053291 is an original dataset announced via ProteomeXchange.
Dataset Summary
Title | A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data |
Description | A core computational challenge in the analysis of mass spectrometry data is the de novo sequencing problem, in which the generating amino acid sequence is inferred directly from an observed fragmentation spectrum without the use of a sequence database. Recently, deep learning models have made significant advances in de novo sequencing by learning from massive datasets of high confidence labeled mass spectra. However, these methods are primarily designed for data-dependent acquisition (DDA) experiments. Over the past decade, the field of mass spectrometry has been moving toward using data-independent acquisition (DIA) protocols for the analysis of complex proteomic samples due to their superior specificity and reproducibility. Hence, we present a new de novo sequencing model called Cascadia, which uses a transformer architecture to handle the more complex data generated by DIA protocols. In comparisons with existing approaches for de novo sequencing of DIA data, Cascadia achieves improved performance across a range of instruments and experimental protocols. Additionally, we demonstrate Cascadia’s ability to accurately discover de novo coding variants and peptides from the variable region of antibodies. |
HostingRepository | PanoramaPublic |
AnnounceDate | 2024-06-21 |
AnnouncementXML | Submission_2024-06-21_17:18:30.512.xml |
DigitalObjectIdentifier | |
ReviewLevel | Non peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Michael MacCoss |
SpeciesList | scientific name: Mus musculus; NCBI TaxID: 10090; scientific name: Homo sapiens; NCBI TaxID: 9606; |
ModificationList | Carbamidomethyl |
Instrument | Orbitrap Astral; Q Exactive HF-X |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2024-06-21 16:54:02 | ID requested | |
⏵ 1 | 2024-06-21 17:18:30 | announced |
Publication List
Justin Sanders, Bo Wen, Paul Rudnick, Rich Johnson, Christine C. Wu, Sewoong Oh, Michael J. MacCoss, William Stafford Noble A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data bioRxiv 2024.06.03.597251 |
doi: https://doi.org/10.1101/2024.06.03.597251 |
Keyword List
submitter keyword: de novo, data independent acquisition, sequence variant, extracellular vesicles, Mag-Net |
Contact List
Michael MacCoss | |
---|---|
contact affiliation | University of Washington |
contact email | maccoss@uw.edu |
lab head | |
Michael MacCoss | |
contact affiliation | University of Washington |
contact email | maccoss@uw.edu |
dataset submitter |
Full Dataset Link List
Panorama Public dataset URI |