NDLI: False-Positive Rate Determination of Protein Target Discovery using a Covalent Modification- and Mass Spectrometry-Based Proteomics Platform

Content Provider	Springer Nature Link
Author	Strickland, Erin C. Geer, M. Ariel Hong, Jiyong Fitzgerald, Michael C.
Copyright Year	2013
Abstract	Detection and quantitation of protein–ligand binding interactions is important in many areas of biological research. Stability of proteins from rates of oxidation (SPROX) is an energetics-based technique for identifying the proteins targets of ligands in complex biological mixtures. Knowing the false-positive rate of protein target discovery in proteome-wide SPROX experiments is important for the correct interpretation of results. Reported here are the results of a control SPROX experiment in which chemical denaturation data is obtained on the proteins in two samples that originated from the same yeast lysate, as would be done in a typical SPROX experiment except that one sample would be spiked with the test ligand. False-positive rates of 1.2-2.2 % and <0.8 % are calculated for SPROX experiments using Q-TOF and Orbitrap mass spectrometer systems, respectively. Our results indicate that the false-positive rate is largely determined by random errors associated with the mass spectral analysis of the isobaric mass tag (e.g., iTRAQ®) reporter ions used for peptide quantitation. Our results also suggest that technical replicates can be used to effectively eliminate such false positives that result from this random error, as is demonstrated in a SPROX experiment to identify yeast protein targets of the drug, manassantin A. The impact of ion purity in the tandem mass spectral analyses and of background oxidation on the false-positive rate of protein target discovery using SPROX is also discussed. Figure ᅟ
Starting Page	132
Ending Page	140
Page Count	9
File Format	PDF
ISSN	10440305
Journal	Journal of The American Society for Mass Spectrometry
Volume Number	25
Issue Number	1
e-ISSN	18791123
Language	English
Publisher	Springer US
Publisher Date	2013-10-10
Publisher Institution	The American Society for Mass Spectrometry
Publisher Place	Boston
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Proteomics Protein-ligand binding Chemical modification Thermodynamics Analytical Chemistry Biotechnology Organic Chemistry Bioinformatics
Content Type	Text
Resource Type	Article
Subject	Spectroscopy Structural Biology

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