PXD051318-2

PXD051318 is an original dataset announced via ProteomeXchange.

Title	A framework for quality control in quantitative proteomics
Description	A thorough evaluation of the quality, reproducibility, and variability of bottom-up proteomics data is necessary at every stage of a workflow, from planning to analysis. We share vignettes applying adaptable quality control (QC) measures to assess sample preparation, system function, and quantitative analysis. System suitability samples are repeatedly measured longitudinally with targeted methods, and we share examples where they are used on three instrument platforms to identify severe system failures and track function over months to years. Internal QCs incorporated at the protein and peptide levels allow our team to assess sample preparation issues and to differentiate system failures from sample-specific issues. External QC samples prepared alongside our experimental samples are used to verify the consistency and quantitative potential of our results during batch correction and normalization before assessing biological phenotypes. We combine these controls with rapid analysis (Skyline), longitudinal QC metrics (AutoQC), and server-based data deposition (PanoramaWeb). We propose that this integrated approach to QC is a useful starting point for groups to facilitate rapid quality control assessment to ensure that valuable instrument time is used to collect the best quality data possible. Data are available on Panorama Public and ProteomeXchange under the identifier PXD051318.
HostingRepository	PanoramaPublic
AnnounceDate	2024-10-01
AnnouncementXML	Submission_2024-10-01_16:59:32.301.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Kristine Tsantilas
SpeciesList	scientific name: Mus musculus; NCBI TaxID: 10090; scientific name: Homo sapiens; NCBI TaxID: 9606; scientific name: Bos taurus; NCBI TaxID: 9913; scientific name: Saccharomyces cerevisiae; NCBI TaxID: 4932;
ModificationList	Label:13C(6)15N(2); Label:13C(6)15N(4)
Instrument	Orbitrap Eclipse; Orbitrap Fusion Lumos; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-04-09 15:13:06	ID requested
1	2024-04-28 12:49:17	announced
⏵ 2	2024-10-01 16:59:33	announced	: Added PubMed Id

Tsantilas KA, Merrihew GE, Robbins JE, Johnson RS, Park J, Plubell DL, Canterbury JD, Huang E, Riffle M, Sharma V, MacLean BX, Eckels J, Wu CC, Bereman MS, Spencer SE, Hoofnagle AN, MacCoss MJ, A Framework for Quality Control in Quantitative Proteomics. J Proteome Res, 23(10):4392-4408(2024) [pubmed]

submitter keyword: quality control, proteomics, mass spectrometry, liquid chromatography, sample preparation, system suitability, quantitative results, PRM, DIA, DDA

Michael MacCoss
contact affiliation	University of Washington
contact email	maccoss@uw.edu
lab head
Kristine Tsantilas
contact affiliation	University of Washington
contact email	ktsantil@uw.edu
dataset submitter

Panorama Public dataset URI