ImmunoPrecipitation Software (IPS™) and ImmunoPrecipitation for MALDI (IPM™)

IPS™ (with the IPM™ Module) is part of the MBS™ bioinformatics package!

IPM™ was developed in collaboration with Doctor Henrik Zetterberg, Doctor Gunnar Brinkmalm, Doctor Erik Portelius, Doctor Ulf Andréasson and Professor Kaj Blennow.

Pre-Extraction Processing

Baseline Subtraction

Baseline Subtraction calculates and removes the baseline signal from each spectrum. Two options are available; 1) calculating the baseline beneath (but along with) all the bottom data points, and 2) calculating the average baseline between the noise area placing half of the noise area above the baseline and half below the baseline (peaks are excluded from the calculation).

Savitzky-Golay Filter

The Savitzky-Golay filter is a popular preprocessing (smoothing) technique often used to reduce the noise and remove narrow spikes in a spectrum.

Peak Extraction

Peak Detection by Custom Peak Integration

Peak Detection by Custom Peak Integration calculates AUC on spectra in custom (user-provided) intervals. Peaks detected using Custom peak Integration are always homogenous between different spectra and do not require using Binning.

Pre-Analysis Processing

Peak Normalization

Peak Normalization calculates the Area Under the Curve for all peaks and divides each peak with the calculated sum, and multiplies it with a specified factor. The sum of all intensities will be equal to the selected value, and the value of 1 (100%) is set as default.

Peak Average Creation

Peak Average Creation calculates the average height of each peak in a set of peaks. The input used to calculate the average peaks must be peak results with peaks in the same location. When two spectra have the same peak of different intensity then an average intensity will be calculated. These two spectra are then replaced with one spectrum containing the average peak intensity.

Data Analysis

Relative Change in Group Comparison

Relative Change in Group Comparison is an analysis where the relative changes in intensities are compared for spectra before and after treatment, and this is performed for three selected groups of spectra (i.e. a disease group, a control group, and a third group). Both graphical tools and formal statistical tests are used. Available tests are: Kruskal-Wallis test with Mann-Whitney test.

Modules & Sub-Modules

IPS™ contains IPM™ and other Modules, and each of them contains several Sub-Modules. A Sub-Module can consist of one or several methods or algorithms.