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Evaluation of advanced precursor determination for tandem mass tag (TMT)-based quantitative proteomics across instrument platforms

ABSTRACT: Myers SA, Klaeger S, Satpathy S, Viner R, Choi J, Rogers J, Clauser K, Udeshi ND, and Carr SA. 2018, J Prot Res. TMT-based quantitation is a strong modality for quantitative proteomics as samples can be multiplexed, creating large-scale data sets with high precision and minimal missing values. However, co-isolation/co-fragmentation of near isobaric, co-eluting precursor peptide analytes has been well documented to show ratio compression, compromising the accuracy of peptide/protein quantitation. Advanced peak determination (APD) is a new peak picking algorithm that shows improved identification of peak detection in survey scans (MS1) to increase the number of precursors selected for unimolecular dissociation (MS2). To increase the number of these features selected for MS2 APD purposefully selects multiple peptide precursors of very similar m/z that often derive from different proteins - a major source of ratio compression in TMT quantification. Here, we evaluate the effects of various data acquisition parameters combined with APD on ratio compression. We find that data acquisition with APD enabled results in more co-isolated precursors, more mixed spectra, and in turn, fewer peptide spectral matches, especially at standard on-column loads. We conclude that APD should not be utilized for isobaric tagging, MS2-based experiments.

INSTRUMENT(S): Orbitrap Fusion Lumos, QExactive HFX

ORGANISM(S): Saccharomyces Cerevisiae (ncbitaxon:4932)

SUBMITTER: Steven A. Carr

PROVIDER: MSV000083005 | MassIVE | Sun Oct 07 09:41:00 BST 2018

REPOSITORIES: MassIVE

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