Glossary of Terms 311
V4.2 LabChip GX User Manual PerkinElmer
Ladder Analysis
A ladder is a mix of compounds of known sizes that is used to
create a size ruler for the samples. Ladder data is used to convert
the migration time of each sample peak into a size for the
compound responsible for that peak. The known sizes of the ladder
compounds are supplied in the assay file and can be viewed in the
Analysis Tab on the Assay Analysis Window.
The initial step in ladder analysis is to identify the most prominent
peaks in the ladder well and associate each peak with the known
ladder sizes. The analyzed ladders provide a table of values
relating size to migration time. Typically the migration time uses the
center of the peak in the ladder and the sample.
Failure to find the correct number of ladder peaks prevents further
analysis of the sample wells using the faulty ladder. The software
automatically attempts to use the nearest good ladder before
generating an analysis error.
A Ladder Quality Score is computed for each Ladder well. The
Ladder Quality Score is the R
2
value for the fit of the peak migration
times to size curve multiplied by 10. If the Ladder Quality Score is
less than the Ladder Rejection Threshold specified on the
Alignment Tab in the Assay Analysis Window, the ladder well
generates an error and is not used for sizing or quantization. The
software will use the nearest good ladder to analyze the samples.
The analysis settings can specify which ladder is used to size any
particular sample row. If more accurate sizing can be obtained by
measuring migration times at the start of each peak, this option can
be selected in the Assay Analysis Window.
Lower Marker
An internal standard that is added to a sample in a well to assist in
determining size and concentration of the sample. For DNA assays,
the marker is the same as the first peak in the DNA ladder. DNA
ladders and samples also contain an Upper Marker. For Protein and
RNA assays, the marker is the same as the first peak in the ladder.
Protein Charge Variant assays do not use ladders or markers.
To Next Page
Loading...
Need help?
General
