pyms-test


SUMMARY

Contains examples of PyMS use given in the User Guide.


CONTENT


Chapter 2 -- GC-MS data file reading and operations
---------

20a/ -- Reading of GC-MS raw data in the JCAMP-DX format, and some
    properties of raw data object. The JCAMP-DX file used in this
    example was generated by GC/MS File Translator Pro (Scientific
    Instrument Services, Inc)

20b/ -- Reading of GC-MS raw data in the ANDI-MS format, and some
    properties of raw data object. The ANDI-MS file used in this
    example was generated by Agilent ChemStation.

20c/ -- Use of data information, info(), function

20d/ -- Illustrates the use of diff() function


Chapter 3 -- GC-MS data structure
---------

30a/ -- Demonstrates building of the intensity matrix from the raw 
    GC-MS data, and some basic methods of the IntensityMatrix

30b/ -- Exploration of build intensity matrix parameters.

30c/ -- Build integer mass intensity matrix using bin boundary of
    -0.3 and +0.7.

31/ -- MassSpectrum and IonChromatogram objects of an IntensityMatrix

32/ -- Saving IonChromatogram and IntensityMatrix information.


Chapter 4 -- Data filtering
---------

40a/ -- Trim raw data retention time/scan range

40b/ -- Crop mass range and ignore given masses

41a/ -- Noise filtering with the mean/median moving window filter, on TIC

41b/ -- Noise filtering with the Savitzky-Golay filter, on TIC

42a/, 42b/ -- TopHat baseline correction

43/ -- A pre-processing of data by ICs (building of the intensity matrix,
    smoothing each IC with the Savitzky-Golay filter and baseline correction
    with the TopHat corrector)


Chapter 5 -- Peaks and Peak detection
---------

50/ -- Demonstrates a Peak object and its properties.

51/ -- Crop mass range and zero mass intensities.

52/ -- Peak detection and deconvolution.

53/ -- Filter list of detected peaks.

54/ -- Peak area.


Chapter 6 -- Peak alignment by dynamic programming.
---------

60/ -- Experiment object.

61a/ -- Experiment setup for group A peak data.

61b/ -- Experiment setup for group B peak data.

62/ -- Alignment of group A peaks.

63/ -- Alignment of peaks within group A, group B and between groups A and B.

64/ -- Peak alignment with the "common ion" filtering.


Chapter 7 -- Plotting.
---------

70a/ -- A simple plot of TIC

70b/ -- A simple overlay plot of multiple ICs
 
71/ -- A plot with Display() object. Example shows an overlay plot of TIC,
    several ICs, and peaks detected by PyMS


Chapter 9 -- Parallel processing with PyMS.
---------

x10/ -- An example of parallel processing of data. Shows how to loop
   over all ICs in an intensity matrix, and perform noise smoothing
   on each IC (in parallel). Please see User Guide for instructions
   how to run this example on multiple CPUs