PXD008259

PXD008259 is an original dataset announced via ProteomeXchange.

Title	Compositional Proteomics: The Effects of Spatial Constraints on Protein Quantification Utilizing Isobaric Tags
Description	Mass spectrometry (MS) has become an accessible tool for whole proteome quantitation with the ability to characterize protein expression across thousands of proteins within a single experiment. A subset of MS quantification methods (e.g., SILAC and label-free) monitor the relative intensity of intact peptides, where thousands of measurements can be made from a single mass spectrum. An alternative approach, isobaric labeling, enables precise quantification of multiple samples simultaneously through unique and sample specific mass reporter ions. Consequently, in a single scan, the quantitative signal comes from a limited number of spectral features (≤11). The signal observed for these features is constrained by automatic gain control, forcing codependence of concurrent signals. The study of constrained outcomes primarily belongs to the field of compositional data analysis. We show experimentally that isobaric tag proteomics data are inherently compositional and highlight the implications for data analysis and interpretation. We present a new statistical model and accompanying software, which improves estimation accuracy and the ability to detect changes in protein abundance. Finally, we demonstrate a unique compositional effect on proteins with infinite changes. We conclude that many infinite changes will appear small and that the magnitude of these estimates is highly dependent on experimental design.
HostingRepository	PRIDE
AnnounceDate	2018-03-27
AnnouncementXML	Submission_2018-03-27_00:33:46.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joao Paulo
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2017-11-22 01:12:58	ID requested
⏵ 1	2018-03-27 00:33:52	announced

O'Brien JJ, O'Connell JD, Paulo JA, Thakurta S, Rose CM, Weekes MP, Huttlin EL, Gygi SP, Compositional Proteomics: Effects of Spatial Constraints on Protein Quantification Utilizing Isobaric Tags. J Proteome Res, 17(1):590-599(2018) [pubmed]

curator keyword: Biological

submitter keyword: Tandem Mass Tags (TMT), Isobaric Tags for Relative and Absolute Quantitation (iTRAQ), Bayesian Hierarchical Modeling, Partially Pooled Variance, Ratio Compression, Interference, SPS-FTMS3, Mass Spectrometry, Infinite Changes, Signal Detection

Steven P. Gygi
contact affiliation	Cell Biology Harvard Medical School USA
contact email	sgygi@hms.harvard.edu
lab head
Joao Paulo
contact affiliation	Harvard Medical School
contact email	joao_paulo@post.harvard.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD008259
     1. Label: PRIDE project
     2. Name: Compositional Proteomics: The Effects of Spatial Constraints on Protein Quantification Utilizing Isobaric Tags