Fig. 2: Choice of spectral library and DIA analysis software influences number of identified proteins. | Nature Communications

Fig. 2: Choice of spectral library and DIA analysis software influences number of identified proteins.

From: Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity

Fig. 2

Protein number, distribution, and variance for each DIA analysis workflow separated by species and color-coded by spike-in condition. Left: Number of all identified and quantified proteins in all 92 samples. Center: Log2 intensity distributions. Right: Log2 variance. Log2 variance values < −12 were excluded from this plot. For spike-condition, 1:6 data of n = 22 biologically independent samples have been used and for each of the other spike-in conditions data of n = 23 biologically independent samples have been used. The boxplots show median (center line), interquartile range (IQR, extending from the first to the third quartile) (box), and 1.5 * IQR (whiskers).

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