Scribd
Upload
49 views

Step by Step Guide

This document provides step-by-step instructions for creating a 3D plot of mass spectrometry data from a MassLynx continuum file in Origin. It involves using DataBridge to convert the raw file to a text file, using EDit to process the text file into a CSV format, and opening the CSV in Origin. In Origin, the file is converted to a matrix and can be plotted as a contour map to visualize the 3D dataset. Contour levels can be adjusted to enhance peaks and remove noise.

Uploaded by

Sourav Saha
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
49 views

Step by Step Guide

This document provides step-by-step instructions for creating a 3D plot of mass spectrometry data from a MassLynx continuum file in Origin. It involves using DataBridge to convert the raw file to a text file, using EDit to process the text file into a CSV format, and opening the CSV in Origin. In Origin, the file is converted to a matrix and can be plotted as a contour map to visualize the 3D dataset. Contour levels can be adjusted to enhance peaks and remove noise.

Uploaded by

Sourav Saha
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
You are on page 1/ 5

Step-by-step instructions

for creating a 3D Origin plot from a MassLynx continuum file



Your mass spectrum will be saved as a series of files in a folder called SAMPLE.raw (where SAMPLE
is your filename).

DataBridge

Open DataBridge:



You will be greeted with the following screen:



Hit Select and browse to your spectrum:




Check that under Options the conversion is set to Source =Masslynx, Target =ASCII:




Hit Convert. The file will be saved as a .txt file, which may now be treated with EDit.


EDit

EDit may be downloaded freely as a .zip file (http://web.uvic.ca/~mcindoe/edesi.html). The file should
be unzipped and saved to disk (EDit.exe). Upon running the program, users will be greeted by the
following dialogue box:



To begin, hit Dimension, and browse to the .txt file previously generated from DataBridge.



The program then fills out the boxes according to the data found in the file:



The top row indicates the start and end values of m/z. Number indicates the number of m/z units
between these two values (in this case, 701 50 =651). If a higher resolution than 1 m/z is required,
increase the Number value accordingly (e.g. for a resolution of 0.5 m/z in this example, change to
1302). The second row similarly computes the number of scans there is no advantage in increasing
the Number setting here (you cant increase the number of scans unless you repeat the experiment)
but in some cases it may be useful to lower the number (e.g. a very weak sample may have had 4 scans
collected per increment in the cone/collision voltage, in which case dividing the Number value by 4
is necessary). Finally, the third row gives the actual retention time rather than scan number, which is
useful if chromatographic information is to be manipulated instead of a variable set to change linearly
with scan number (as is the case for ED spectra).

The two Number settings give the size of the matrix, in this case 651 151. Hitting Process allows
you to choose the same .txt file and to perform the conversion to .csv format with the appropriate
settings. Save the .csv file; it is now ready for processing using your scientific graphing package.

The Integrate m/z option sums up all of the intensity samples collected for every m/z within the range
of the output bin. When the m/z data are not equally distributed, this can result in more samples
being integrated in one region (e.g. at low m/z) than another (e.g. at high m/z). This is usually the
desired result, this conserves all data within the range. However, for some applications it may be
desirable to divide by the number of samples collected within the m/z bin, thus an averaging rather
than an integrating behaviour. In this case deselect the Integrate m/z option. Note that in all cases,
scans are averaged if there is more than one scan in an output bin.

The Normalise option simply scales all of the output data to the highest (absolute) value observed in
the data (after integration or averaging described above). Thus the data lie on a known scale from 0 to
1.

Origin
Click on File, and Open. In the first dialog box under Files of type: choose ASCII Data
(*.dat, *.csv, *.txt). Browse to the .csv file you saved as output from the EDit program:


The open file must be converted into the special Origin matrix format in order to plot 3D graphs. Select
Edit, Convert to Matrix and Direct. Click on the radio button for Y varies across columns
and check the boxes for Y values in first row and X values in first column:



The resulting matrix (the data appears with a yellow background) may be plotted in a variety of styles,
but the best place to start is probably a simple contour map:



The initial plot will probably appear nonsensical until Speed Mode is switched off (the matrix is
usually a large one). Go to Format, Layer, go to the Size/Speed tab and uncheck the box
labelled Matrix data, maximum points per dimension.

Origin automatically assigns contour lines to particular values; like all other features of the graph, these
may be altered to suit. Generally, users will want to enhance the lower intensity peaks. Double-click on
any peak in the spectrum, and you will be greeted by the following dialog box:



Double-click on the value under Level and enter a smaller value. Other contour lines may be added,
subtracted or adjusted to suit the desired picture. Maximising real signals while leaving out noise is the
primary goal.

Relabel the x axis m/z, and the y axis with whatever parameter is appropriate, e.g. cone voltage,
collision voltage, time, etc.

You might also like