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PXD022659

PXD022659 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleImproving SILAC quantification with data independent acquisition to investigate bortezomib-induced protein degradation
DescriptionStable isotope labeling by amino acids in cell culture (SILAC) coupled to data-dependent acquisition (DDA) is a common approach to quantitative proteomics with the desirable benefit of reducing batch effects during sample processing and data acquisition. More recently, using data-independent acquisition (DIA/SWATH) to systematically measure peptides has gained popularity for its comprehensiveness, reproducibility, and accuracy of quantification. The complementary advantages of these two quantitative techniques logically suggests combining them. Here, we develop a SILAC-DIA-MS workflow using free, open-source software. We determine empirically that using DIA achieves similar peptide detection numbers as DDA and that DIA improves the quantitative accuracy and precision of SILAC by an order of magnitude. Finally, we apply SILAC-DIA-MS to determine protein turnover rates of cells treated with bortezomib, an FDA-approved proteasome inhibitor for multiple myeloma and mantle cell lymphoma, where we observe that SILAC-DIA produces more sensitive protein turnover models. Of the proteins determined differentially degraded by both acquisition methods, we find known ubiquitin-proteasome degrands such as HNRNPK, EIF3A, and IF4A1/EIF4A-1, and a slower turnover for CATD, a protein implicated in invasive breast cancer. With improved comprehensive quantification from DIA, we anticipate making SILAC-based experiments more sensitive and reproducible, especially pulse chase SILAC for protein turnover.
HostingRepositoryPanoramaPublic
AnnounceDate2020-11-24
AnnouncementXMLSubmission_2020-11-24_10:27:26.xml
DigitalObjectIdentifier
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterLindsay Pino
SpeciesList scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationListCarbamidomethyl; Label:13C(6)15N(2); Label:13C(6)15N(4)
InstrumentQ Exactive HF-X; TripleTOF 6600
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-11-22 13:04:36ID requested
12020-11-24 10:27:26announced
Publication List
Pino LK, Baeza J, Lauman R, Schilling B, Garcia BA. Improved SILAC quantification with data independent acquisition to investigate bortezomib-induced protein degradation. bioRxiv [Internet]. 2020 Jan 1;2020.11.23.394304. Available from: http://biorxiv.org/content/early/2020/11/23/2020.11.23.394304.abstract
Keyword List
submitter keyword: protein turnover, SILAC, protein degradation, data independent acquisition, quantitative proteomics, SILAC-DIA
Contact List
Lindsay Pino
contact affiliationUniversity of Pennsylvania
contact emaillindsay.pino@gmail.com
lab head
Lindsay Pino
contact affiliationUniversity of Pennsylvania
contact emaillindsay.pino@gmail.com
dataset submitter
Full Dataset Link List
Panorama Public dataset URI