474. MS data, part I: Exporting data as csv from wsearch32, and generating MS assignments using Matt Monroe's molecular weight calculator

NOTE: I've heard rumours about problems with wsearch on Windows 7 Home, and on Windows 8. I've heard reports of it working on Windows 7 Professional. Curiously, it works just fine on linux under wine.

This post is written with two particular students in mind. I could put this in a pdf and email it, but why not share with the wider world since other people may encounter the same issues?

See here for part II: http://verahill.blogspot.com.au/2013/07/480-ms-data-part-ii-plotting-and.html

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1. Exporting data from wsearch32
To install wsearch32 under wine, see here: http://verahill.blogspot.com.au/2013/01/321-wsearch32-in-wine.html

In order to export data from wsearch so that you can plot it in e.g. gnuplot, octave, origin or excel, do the following:

Open a spectrum (chromatogram) and pick a slice, then click on the M/I icon in the bottom right:

 Pick Save As

 And save as e.g. csv (comma separated file)

Done.

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2. Using formula finder in Matthew Monroe's Molecular Weight Calculator
To install the molecular weight calculator in wine, see here: http://verahill.blogspot.com.au/2012/09/matt-monroes-molecular-weight.html

Open the molecular weight calculator and go to edit abbreviations.

 Add an abbreviation for MeO. We'll call it Methx, and it has a charge of -1:

 Methanol:

 Nitrate:

 Hit OK to save the changes.

 Go to formula finder:

We'll be looking for Ga, NO3, MeOH, O, H, MeO. Then click on Formula Finder Options:

 Limit the charge to 1:

 And search:

You can do fancier stuff, e.g. searching directly for the m/z and bound the search to min/max amounts of different elements:

 As shown here:

320. Wsearch32 in Wine

Wsearch32 is a windows program that does what it's supposed to -- open mass spectrometer data files. Because our students use it quite a lot and to save me time in training them, here's how to install wsearch32 and how to get started with it. It runs almost perfectly in Wine.

One notable thing about Wsearch is that it opens HP Agilent Chemstation .D files without any problems. It's notable because different versions of HP Agilent Chemstation can't even open files written by other versions (yup, it's true...) of the same damned program.

Another obvious advantage of Wsearch is that it makes it very easy to export data, although it only exports one spectrum at a time (i.e. you can't get the full time-dependent data set).

WSearch was written by Frank Antolasic at the RMIT in Melbourne, Australia.


What doesn't work under Wine: It will freeze if you try to open several files at the same time. This does not happen on native Windows.

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Installation
Download it from here: http://www.wsearch.com.au/

wget http://www.wsearch.com.au/wsearch32/wsearch32.zip
unzip wsearch32.zip

and follow the instructions:

There's nothing odd about the installation process

It works as well as under windows

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Screenshots

This is the default view

Click on the import icon (the red one in the left corner), and select your file. There are plenty of supported formats.

This is the TIC view. Click anywhere on the TIC to get the corresponding spectrum

TIC and spectrum view.

Click on the M/I icon on the right to get a list of all the data in the spectrum plot..

You can then save the spectrum in a range of ascii based formats.

You can get the acquisition headers under Chromatogram/List header info. You can also make ion plots  in the same menu.

Wsearch also comes with a simple isotopic pattern calculator.

The Help works fine under linux/wine

This is the free version of wsearch -- there is some functionality missing.