freeQuant: A Mass Spectrometry Label-Free Quantification Software Tool for Complex Proteome Analysis

Figure 4

The protein abundance fold change of quantitative algorithm. Quantitative algorithms based on MS abundance features were involved. NSAF by spectral count and NSAF by total ion counts were used to quantify the whole protein dataset (a), proteins only with shared peptides (b), and proteins only with distinct peptides (c), respectively. It shows that the dynamical range of MS/MS TIC coupled with spectral count is broader than NSAF (d). Therefore, MS/MS TIC coupled with spectral count which alleviates this particular deficiency arising from SC was more suitable for determining protein abundance fold change. For panels (a), (b), and (c), the -axis represents the two quantitative algorithms, NSAF by spectral count (NSAF_SC) and NSAF by TIC (NSAF_TIC); the -axis represents the quantitative results of NSAF_SC or NSAF_TIC, which are calculated by Formula (1) and Formula (3) in Section 2.2, separately. The quantitative results are shown in log₁₀ format.

(a) Evaluation of the whole proteins

(b) Evaluation of proteins only with shared peptides

(c) Evaluation of proteins only with distinct peptides

(d) The table of dynamical range of different samples based on NSAF_SC and NSAF_TIC