PXD053291

PXD053291 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-21 16:54:02	ID requested
⏵ 1	2024-06-21 17:18:30	announced

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

submitter keyword: de novo, data independent acquisition, sequence variant, extracellular vesicles, Mag-Net

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

Panorama Public dataset URI