High-Throughput Proteome Profiling of Plasma and Native Plasma Complexes Using Native Chromatography

We describe a high-throughput method for co-fractionation mass spectrometry (CF-MS) profiling for native plasma protein profiling. CF-MS allows the profiling of endogenous protein complexes between samples. Proteins often interact with other proteins and form macromolecular complexes that are different in disease states as well as cell states and cell types. This protocol describes an example for the sample preparation of 954 individual size exclusion chromatography (SEC) fractions, derived from 18 plasma samples that were separated into 53 fractions. Eighteen plasma samples were chosen based on the TMTpro multiplexing, but this methodology can be adapted for fewer or larger numbers of samples as appropriate. Our automated sample preparation method allows for high-throughput native plasma profiling, and we provide detailed methods for both a label-free and an isobaric labeling approach, discuss the merits of each approach, and detail the advantages of combining these strategies for comprehensive native plasma proteome profiling.

Isobaric labeling: Expanding the breadth, accuracy, depth, and diversity of sample multiplexing

Isobaric labeling has rapidly become a predominant strategy for proteome-wide abundance measurements. Coupled to mass spectrometry, sample multiplexing techniques using isobaric labeling are unparalleled for profiling proteins and posttranslational modifications across multiple samples in a single experiment. Here, I highlight aspects of isobaric labeling in the context of expanding the breadth of multiplexing, improving quantitative accuracy and proteome depth, and developing a wide range of diverse applications. I underscore two facets that enhance quantitative accuracy and reproducibility, specifically the availability of quality control standards for isobaric labeling experiments and the evolution of data acquisition methods. I also emphasize the necessity for standardized methodologies, particularly for emerging high-throughput workflows. Future developments in sample multiplexing will further strengthen the importance of isobaric labeling for comprehensive proteome profiling.