Comparison of Protein Quantification in a Complex Background by DIA and TMT Workflows with Fixed Instrument Time

Label-free quantification (LFQ) and isobaric labeling quantification (ILQ) are among the most popular protein quantification workflows in discovery proteomics. Here, we compared the TMT SPS/MS3 10-plex workflow to a label free single shot data-independent acquisition (DIA) workflow on a controlled s...

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Veröffentlicht in:Journal of proteome research 2019-03, Vol.18 (3), p.1340-1351
Hauptverfasser: Muntel, Jan, Kirkpatrick, Joanna, Bruderer, Roland, Huang, Ting, Vitek, Olga, Ori, Alessandro, Reiter, Lukas
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Sprache:eng
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Zusammenfassung:Label-free quantification (LFQ) and isobaric labeling quantification (ILQ) are among the most popular protein quantification workflows in discovery proteomics. Here, we compared the TMT SPS/MS3 10-plex workflow to a label free single shot data-independent acquisition (DIA) workflow on a controlled sample set. The sample set consisted of ten samples derived from 10 biological replicates of mouse cerebelli spiked with the UPS2 protein standard in five different concentrations. For a fair comparison, we matched the instrument time for the two workflows. The LC–MS data were acquired at two facilities to assess interlaboratory reproducibility. Both methods resulted in a high proteome coverage (>5000 proteins) with low missing values on protein level (
ISSN:1535-3893
1535-3907
DOI:10.1021/acs.jproteome.8b00898