MS3 eliminates ratio distortion in isobaric labeling-based multiplexed quantitative proteomics

By Lily Ting, R. Rad, Steven P. Gygi, W. Haas. Nature Methods, 2011

670 citations recorded by the source corpus.

Quantitative mass spectrometry–based proteomics is highly versatile but not easily multiplexed. Isobaric labeling strategies allow mass spectrometry–based multiplexed proteome quantification; however, ratio distortion owing to protein quantification interference is a common effect. We present a two-proteome model (mixture of human and yeast proteins) in a sixplex isobaric labeling system to fully document the interference effect, and we report that applying triple-stage mass spectrometry (MS3) almost completely eliminates interference.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/bcfa7991b7e3ad3480b4f838db645830776d09e9

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Citations in the corpus

Lysine succinylation is a frequently occurring modification in prokaryotes and eukaryotes and extensively overlaps with acetylation. (2013, background): “Quantification of TMT mass tags may be inaccurate if additional peptides are coisolated with the targeted peptide ion (Ting et al., 2011).”
Obesity shapes metabolism in the tumor microenvironment to suppress anti-tumor immunity (2020, methodology): “Each analysis used an SPS-MS3-based TMT method (McAlister et al., 2014; Ting et al., 2011), which has been shown to reduce ion interference compared to MS2-based quantification (Paulo et al.”
An insight into iTRAQ: where do we stand now? (2012, methodology): “Strategies employing MS level simplification were also recently reported in back to back papers [31, 32] in Nature Methods with an accompanying ‘News and Views’ article [51], which discusses these Orbitrap-based method developments in detail.”
Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, positive): “A promising alternative procedure using multistage MS3-based scans eliminates this interference (Ting et al., 2011).”
Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial (2018, positive): “…in reporter ions from co-eluting and co-fragmenting peptides, this has been addressed to some extent by using optimized data acquisition and analysis meth-ods (Ting et al , 2011; Savitski et al , 2013; McAlister et al , 2014; Ahrne et al , 2016; O’Brien et al , 2018; Sonnett et al , 2018).”