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. 2017:1619:339-352.
doi: 10.1007/978-1-4939-7057-5_23.

Efficient Quantitative Comparisons of Plasma Proteomes Using Label-Free Analysis with MaxQuant

Lynn A Beer  1 , Pengyuan Liu  1 , Bonnie Ky  2 , Kurt T Barnhart  3 , David W Speicher  4
Affiliations

Efficient Quantitative Comparisons of Plasma Proteomes Using Label-Free Analysis with MaxQuant

Lynn A Beer et al. Methods Mol Biol. 2017.

Abstract

Mass spectrometry (MS)-based quantitation of plasma proteomes is challenging due to the extremely wide dynamic range and molecular heterogeneity of plasma samples. However, recent advances in technology, MS instrumentation, and bioinformatics have enabled in-depth quantitative analyses of very complex proteomes, including plasma. Specifically, recent improvements in both label-based and label-free quantitation strategies have allowed highly accurate quantitative comparisons of expansive proteome datasets. Here we present a method for in-depth label-free analysis of human plasma samples using MaxQuant.

Keywords: Label-free quantitation; MaxQuant; Plasma biomarkers; Proteomics.

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Figures

Fig. 1
Fig. 1
Comparison of label-free and TMT protein quantitation for ADAM12, a known ectopic pregnancy biomarker. (a) Label-free quantitaion of a 4 hr LC-MS/MS run for triplicate depletions using IGY14-Supermix columns of pooled plasma from individuals having an ectopic pregnancy (EP), normal intrauterine pregnancy (IUP), or spontaneous abortion (SAB). Normalized LFQ protein intensity for ADAM12 is shown. (b) 10-plex TMT labeling of the same triplicate pooled plasma samples. Summed intensities of measured peak m/z values for the TMT reporter ions representing ADAM12 are shown.
Fig. 2
Fig. 2
Coefficients of variation of protein identifications for a comparison of label-free and TMT quantitation. (a) 10-plex TMT labeling of pools of EP, IUP, and SAB plasma that were depleted in triplicate using IGY14-Supermix columns. (b) Label-free quantitation of the same triplicate pooled plasma samples. “Total Protein” values indicated represent numbers of protein groups across all samples identified by 2 or more peptides and with peptide and protein FDR of 1%. “CV <30% or <10%” values represent averages of the three groups of samples (EP, IUP, SAB).
Fig. 3
Fig. 3
Summed protein intensities for all protein groups before (Intensity, left) and after (LFQ Intensity, right) normalization. Single 4h LC-MS runs of triplicate pools of IGY14-Supermix depleted EP, IUP, and SAB plasma were quantitated in a label-free analysis using MaxQuant, with “match between runs” enabled.
See this image and copyright information in PMC

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