Optimizing Accuracy and Depth of Protein Quantification in Experiments Using Isobaric Carriers

• DOI: 10.1021/acs.jproteome.0c00675
• Publication Date: 2020-11-14T14:51:29Z
• Authors: Harrison Specht; Nikolai Slavov
• Keywords: Isobaric process; Isobaric labeling; Proteome

The isobaric carrier approach, which combines small isobarically labeled samples with a larger sample, finds diverse applications in ultrasensitive mass spectrometry analysis of very samples, such as single cells. To enhance the growing use carriers, we characterized trade-offs using carriers controlled experiments complex human proteomes. data indicate that directly peptide sequence identification without simultaneously increasing number protein copies sampled from samples. results also strategies for optimizing amount and analytical parameters, ion accumulation time, different priorities improved quantification or an increased identified proteins. Balancing these enables adapting to applications, quantifying proteins limited biopsies organoids, building single-cell atlases, modeling networks In all cases, reliability should be estimated incorporated subsequent analyses. We expect guidelines will aid explicit incorporation experimental designs transparent error propagation analysis.