Trace: properties and methods

Introduction

Trace is aimed at any two-dimensional data. It is used to stored MS spectrum, either profile or centroid format, but also total ion profile (TIP), base peak profile (BPP) or any other two dimensional representations.

General Properties

• .Title Title of the Trace
• .FigureTitle Title to be displayed in the figure Title
• .TraceType Type of trace. The possibilities are SEP - Chromatogram, electropherogram or any separation profile; CTR - MS centroid scan; PRF - MS profile scans; OTR - Other
• .AxisX Information about the x-axis (label, unit precision)
• .AxisY Information about the y-axis (label, unit precision)
• .Path2Fin Path to the Finnee folder if related to one, otherwise empty
• .AdiParam Structure that can be used to store any supplementary information.

Data

The data can either be stored within the object or in a binary files. The data storage type is defined by the .DataStorage properties.

.DataStorage is 'None'

The Data properties is empty but all other information exist.

.DataStorage is 'inTrace'

The property .storedData should contain a nx2 array of reals with in first column, the axis, and in second column the corresponding values

.DataStorage is 'inFile'

The following properties should be used:

• .Precision Precision of the floating point in the binary file. Either 'single' or 'double'.
• .Path2Dat The path to the binary file where the data are stored
• .Index a 2x1 array of integer, starting and ending position in bit of the data in the binary file.

Dependent properties

• .Data A nx2 array of reals with in first column, the axis, and in second column the corresponding values.
• .InfoTrc A structure with the Ganeral properties
• .bz Bit size: 4 if .Precision is 'single', 8 if .Precision. is 'double'

Methods

Trace

Creator method

plot

plot the trace:

thisTrace.plot

(Some tutorials on Matlab visual exploration of figures here)

extrapolMZ

Should only be used if .TraceType is 'PRF', extrapolate the mz axis for missing values.

[mzAxis, r2, data4axis] = thisScan.extrapolMZ(n, Lim)

where n is the order of the polynomial used to extrapolate the values (default n = 3) and Lim are the mz limits (default Lim = [0 inf]). mzAxis is the full axis, r2 is the Pearson correlation coefficient between the real axis and the extrapolated axis, and data4axis are the data used.

scatter(data4axis(:,1), data4axis(:,2));
xlabel('m/z');
ylabel('Dm/z');

TO BE DONE

Trace should also include methods allowing to analyse the peaks (base line correction, deconvolution, peak picking...)

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