LabChip GX/GXII User Manual

Data Analysis 41How the Software Analyzes Protein Data(Continued)NOTEThe software performs alignment by default. Turning alignment offsuspends data evaluation until you turn it on again.7 Before calculating either the protein size or concentration, thesample data is processed relative to the two ladders thatbracket every 12 samples. First, all of the data is aligned to thelower marker and then stretched, relative to the highestmolecular weight protein in the ladder.8 The concentration of the sample proteins is determined relativeto the bracketed ladders. There are seven proteins in the ladder(not including the lower marker). The ladder concentration isspecified in the assay and cannot be changed. View the settingson the Analysis Tab of the Assay Analysis Window (seepage 156).NOTES• The seven proteins are assumed to represent the averagestaining behavior of proteins and are used to determine anaverage peak area per g/mL of protein. This factor is used toconvert sample peak areas into relative concentration. The totalrelative concentration of all proteins is calculated by addition ofthe relative concentration of the individual proteins and isdisplayed in the Well Table View (see page 140).• Since the conversion factor is determined for each ladder, thefactor can be linearly interpolated for each sample and thusaccount for any assay drift.• The software allows you to define the lower marker. Changingthe selection of the marker will lead to quantitative changes inthe calibration procedure, and therefore in the entire dataevaluation.P/N 127170 Rev. 00 LabChip GX User Manual Caliper Life Sciences, Inc.