Datasets: properties and methods

Introduction

Datasets are a collection of MSscans that described the separation and aquisition. The Finnee object can hold many datasets, while the first dataset will be made by the recording of the MS scans as a function time, Finnee allows manipulating the data in order to improve the quality of information. Each transformation will be recorded in a new dataset.

Properties

• .Title Self-explanatory
• .Log A recording of all transformations that were done to obtain this dataset
• .DateOfCreation Self explanatory
• .Format Format of the MS scans (centroid' or 'profile'
• .BPP A Trace object, the base peak profile; the maximum intensity of each MS scan
• .TIP A Trace object, the total ion profile; the sum intensity of each MS scans
• .TIS A Trace object, the total ion spectrum; only available if a common m/z axis exists. The sum of all MS scan
• .FIS A Trace object, the frequency ion spectrum; only available if a common m/z axis exists. The number of non-zero values at every m/z increment.
• .BIS A Trace object, the base iso spectrum; only available if a common m/z axis exist., the maximum intensity at every m/z increment.
• .LAST A blank Trace object
• .ListOfScans An array of Trace Object. The MS scans.
• .Options4crt Information on the function used to create the dataset
• .Path2Dat The list of all dat files linked to the Trace objects.
• .AxisX Information about the x-axis (label, unit precision, and data for the axis)
• .AxisY Information about the y-axis (label, unit precision and data for teh axis)
• .AxisZ Information about the z-axis (label, unit precision)
• .tol4MZ m/z tolerance
• .MZLim a 2x1 array with the lowest m/z value and highest m/z value
• .Path2Fin Full path to the Finnee object
• .AddInfo A structure used to store additional information

Methods

Dataset

Creator method

getProfile

getProfile allows to create a new trace that will contain the information related to the extracted ion profiles (EIP) within a set m/z interval. For example, with myDataset being a valid Dataset (see Finnee: properties and methods for more information on how to create a dataset). The EIP between mz1 and mz2 will be obtained using the following command:

EIP = myDataset.getProfile([mz1 mz2]);

EIP is a trace object with all associated properties and functions. For example,

EIP.plot

or

EIP.Data

The getProfile command may be run with various options. The general command is as follow:

myFinnee = myDataset.getProfile([mz1 mz2], options1, param1, options1, param2,...)

• 'XLim'. param is a 2x1 array of reals. param(1) is the starting time at which the EIP should be recorded and param(2) the ending time.

getSpectra

getSpectra allows to create a new trace that will contain a spectra or a sum of spectra obtained bwteen a set time interval. For example, with myDataset being a valid Dataset (see Finnee: properties and methods for more information on how to create a dataset). The following command:

Spc = myDataset.getSpectra([t1 t2]);

Spc is a trace object with all associated properties and functions. For example,

Spc.plot

or

Spc.Data

The getProfile command may be run with various options. The general command is as follow:

myFinnee = mmyDataset.getSpectra(options1, param1, options1, param2,...)

• ''.

Tutorials

Object oriented programming allows to easily develop small scripts to tailor the analysis to specific need. Below an example is given allowing to obtained a series of EIP.

Targeted analysis

MZ is a 2xn array, with in the first column the accurate masses and in the second column the migration time of a series of markers. To obtain the EIP, the following script can be used

Dmz         = 0.1;      % mz interval
Dt          = 2;        % time interval
listProfile = {};       % empty array of profiles

for ii = size(MZ, 1)
   listProfile{ii} =  myDataset.getProfile([MZ(ii,1)-Dmz MZ(ii,1)+Dmz], 'XLim',  [MZ(ii,2)-Dt MZ(ii,2)+Dt]);
end

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