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PXD051072

PXD051072 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleInserting Pre-Analytical Chromatographic Priming Runs Significantly Improves Targeted Pathway Proteomics With Sample Multiplexing
DescriptionGoDig, a platform for targeted pathway proteomics without the need for manual assay scheduling or synthetic standards, is a powerful, flexible, and easy-to-use method that uses tandem mass tags (TMT) to increase sample throughput up to 18-fold relative to label-free methods. Though the protein-level success rates of GoDig are high, the peptide-level success rates are more limited, hampering assays of harder-to-quantify proteins and site-specific phenomena. To guide the optimization of GoDig assays as well as improvements to the GoDig platform, we created GoDigViewer, a new stand-alone software that provides detailed visualizations of GoDig runs. GoDigViewer guided the implementation of “priming runs,” an acquisition mode with significantly higher success rates. In this mode, two or more chromatographic priming runs are automatically performed to improve the accuracy and precision of target elution orders, followed by analytical runs which quantify targets. Using priming runs, success rates exceeded 97% for a list of 400 peptide targets and 95% for a list of 200 targets that are usually not quantified using untargeted mass spectrometry. We used priming runs to establish a quantitative assay of 125 macroautophagy proteins that had a >95% success rate and revealed differences in macroautophagy expression profiles across four human cell lines.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_06:35:58.676.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterSteven Shuken
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListTMT6plex-126 reporter+balance reagent acylated residue
InstrumentOrbitrap Eclipse
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-03-28 13:32:11ID requested
12024-04-12 08:52:39announced
22024-10-22 06:35:59announced2024-10-22: Updated project metadata.
Publication List
10.1021/ACS.JPROTEOME.4C00096;
Keyword List
submitter keyword: isobaric labeling, intelligent data acquisition, macroautophagy,Targeted proteomics, chromatography, instrument API, quantitative mass spectrometry, real-time search, pathway proteomics, tandem mass tags
Contact List
Steven P. Gygi
contact affiliationDepartment of Cell Biology, Harvard Medical School
contact emailsteven_gygi@hms.harvard.edu
lab head
Steven Shuken
contact affiliationDepartment of Cell Biology, Harvard Medical School
contact emailsteven_shuken@hms.harvard.edu
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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