PXD022390

PXD022390 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Evaluation of differential peptide loading on TMT-based proteomic and phosphoproteomic data quality
Description	Investigating the impacts on MS data quantitation reproducibility when loading differential amounts of peptides, ranging from 20 to 400 ug, across channels of TMT 11 multiplexes. PTRC_Exp9 files represent global proteome and phosphoproteome data generated from PBMCs isolated from AML patients, acquired through 12 fractions and 6 fractions per plex, respectively. In this experiment, TMT channels were loaded with varying peptide quantities ranging from 20 to 400 ug. PTRC_Exp12 files represent proteomic and phosphoproteomic data from the MOLM-14 AML cell line, also acquired across 12 global proteomics fractions and 6 phosphoproteomics fractions per plex. In this experiment, all TMT channels were loaded with equivalent quantity of peptides (400 ug). Samples were reduced with dithiothreitol, alkylated with iodoacetamide, and double-digested with Lys-C and trypsin. Digested peptides were desalted with C18 SPE columns, labeled with TMT11 isobaric tags, and fractionated by high pH reverse phase separation. After aliquots were removed for global proteomics (12 fractions per plex), samples were concatenated and IMAC was used to enrich phosphopeptides (6 fractions per plex). LC-MS/MS measurements were acquired on an Orbitrap Fusion Lumos mass spectrometer.
HostingRepository	MassIVE
AnnounceDate	2022-08-16
AnnouncementXML	Submission_2022-08-16_10:05:38.700.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Matthew Monroe
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	Oxidation; Carbamidomethyl; TMT6plex
Instrument	Orbitrap Fusion Lumos

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-05 18:35:57	ID requested
⏵ 1	2022-08-16 10:05:39	announced

Publication List

Sanford JA, Wang Y, Hansen JR, Gritsenko MA, Weitz KK, Sagendorf TJ, Tognon CE, Petyuk VA, Qian WJ, Liu T, Druker BJ, Rodland KD, Piehowski PD, Evaluation of Differential Peptide Loading on Tandem Mass Tag-Based Proteomic and Phosphoproteomic Data Quality. J Am Soc Mass Spectrom, 33(1):17-30(2022) [pubmed]

Sanford JA, Wang Y, Hansen JR, Gritsenko MA, Weitz KK, Sagendorf TJ, Tognon CE, Petyuk VA, Qian WJ, Liu T, Druker BJ, Rodland KD, Piehowski PD, Evaluation of Differential Peptide Loading on Tandem Mass Tag-Based Proteomic and Phosphoproteomic Data Quality. J Am Soc Mass Spectrom, 33(1):17-30(2022) [pubmed]

Keyword List

submitter keyword: AML, TMT, clinical proteomics, phosphoproteomics

submitter keyword: AML, TMT, clinical proteomics, phosphoproteomics

Contact List

Paul Piehowski
contact affiliation	Pacific Northwest National Laboratory
contact email	Paul.Piehowski@pnnl.gov
lab head
Matthew Monroe
contact affiliation	Pacific Northwest National Laboratory
contact email	matthew.monroe@pnnl.gov
dataset submitter

Full Dataset Link List

MassIVE dataset URI
Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive.ucsd.edu/MSV000086417/

MassIVE dataset URI

Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive.ucsd.edu/MSV000086417/