Figure 6. Dynamic MS detection range of recombinant Thy-1.

(A) Recombinant Thy-1 1D SDS PAGE dilution experiment (43.34 kDa, mass migration area highlighted by arrow; D1 = 0.3, D2 = 0.24, D3 = 0.18, D4 = 0.12, D5 = 0.06, D6 = 0.03 μg; N = 3 replicate runs). Thy-1 content <0.12 μg is not visible by CBB staining. (B) Dynamic MS range of recombinant Thy-1 (50% of gel content is introduced to the LC MS system for technical reasons; therefore the X-axis displays corrected values) generated by MaxQuant software LC MS detection threshold can be determined <0.03 μg describing intensity values < 1*E⁶, whereby the LFQ value is calculated zero. (C). Separate evaluation of the Thy-1 specific peptides (P1–P5) indicating that for Thy-1 content <0.03 μg only two Thy-1 specific peptides can be detected (P1 & 3; highlighted by asterisk); which represent MS/MS identification peptides in study sample runs. Since in sample runs only two of five characteristic peptides (P1 & P3) could be detected showing raw output values <1*E⁶, Thy-1 can be attributed to the low detection range and is consequently underrepresented in the retina samples leading to critical quantification output.