Applied Biosystems 3500 User Manual

Setting
Description
Smoothing Select an option to smooth the outline of peaks and reduce the number of
false peaks detected:
• None (default) to apply no smoothing. Best if the data display sharp,
narrow peaks of interest.
• Light to provide the best results for typical data. Light smoothing slightly
reduces peak height.
• Heavy for data with very sharp, narrow peaks of interest. Heavy
smoothing can significantly reduce peak height.
Baseline Window Specify a window to adjust the baseline signals of all detected dye colors to
the same level for an improved comparison of relative signal intensity. Note
the following:
• A small baseline window relative to the width of a cluster, or grouping of
peaks spatially close to each other, can result in shorter peak heights.
• Larger baseline windows relative to the peaks being detected can create
an elevated baseline, resulting in peaks that are elevated or not resolved
to the baseline.
Min. Peak Half Width Specify the minimum full peak width at half maximum Peak Height required
for peak detection. The range is 2 to 99 data points.
Polynomial Degree Polynomial Degree cannot be greater than Peak Window Size.
Adjust to affect the sensitivity of peak detection. You can adjust this
parameter to detect a single base pair difference while minimizing the
detection of shoulder effects and/or noise.
The peak detector calculates the first derivative of a polynomial curve fitted
to the data within a window that is centered on each data point in the analysis
range.
Using curves with larger polynomial degree values allows the curve to more
closely approximate the signal and, therefore, captures more of the peak
structure in the electropherogram.
Peak Window Size Enter a window width in data points for peak detection sensitivity. If more
than one peak apex is within the window, all are labeled as a single peak.
Note the following:
• The maximum value is the number of data points between peaks.
• The Peak Window Size setting is limited to odd numbers.
To increase peak detection sensitivity: Increase polynomial degree, decrease
peak window size. To decrease peak detection sensitivity: Decrease
polynomial degree, increase peak window size.
Chapter 7 Manage library resources
Sizecalling protocols library (primary analysis—fragment)
7
3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1
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Applied Biosystems 3500 Specifications

General

Number of capillaries	8
Capillary Length	50 cm
Laser	Solid-state laser
Instrument Type	Capillary electrophoresis system
Technology	Capillary Electrophoresis (CE)
Weight	95 kg
Power Requirements	100–240 V