1: Upload Data

2: Analysis

3: When ready, start the workflow with Execute Workflow button

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Total Peak Area

Total Area is the sum of all integrated signals for that peptide. For example if performing targeted MS/MS with an MS1 scan - this number is the sum of fragment ions and precursor ions

Retention Time

Retention time apex of each targeted peptide


The width at half height of the elution profile

Peak Asymmetry

Calculated by taking 2*a/(a+b). Optimal value is around 1 for a Gaussian peak


Mass Measurement Accuracy of each targeted peptide as reported by Skyline

Fragmentation Efficiency

If performing targeted MS2 or parellel reaction monitoring with a dedicated MS1 scan, then this metric takes the ratio of the summed fragment ion intensity divided by the precursor ion intensity

Control Charts

Basic single metric control charts where green, brown, and bold red lines represent 1, 2, and 3 standard deviations away from the empirically determined mean based on the user entered number of standards to determine thresholds. The green points represent the user-defined reference set while points colored red are outside the 3sd threshold

Pareto Plot

Counts the number of QC runs from each univariate metric outside +/- 3 standard deviations from the empirically derived mean and displays them in a cumulative bar graph

Principal Component Plot

A plot of each QC run in principal component space using the two PCs with the highest variance. A minimuim convex polygon is drawn around the user defined reference set. It describes all variability in PCA space resulting from the reference set.

Multivariate Control Chart

The centroid of the convex hull is calculated and the euclidean distance in PCA space from this centroid to every QC run is plotted as a function of QC run

Mean Fragment Plot

The average of all peptide's fragmentation efficiency metrics are plotted