PAT for Windows

It was written by Dr. Bruce W. Tattershall, Lecturer in Chemistry at the University of Newcastle, England.

Preface

The present author had the experience of running a taught drylab class of about 40 students, in which all of the students were trying to calculate complex isotope patterns using the same web-based application at the same time.  The web server concerned ground progressively to a halt, and since it belonged to a different university, we could do nothing about it.  Our students, being experienced web users, soon discovered a variety of alternative web applications, and spread their efforts to web servers around the world.  Some programs simply would not cope with the examples from inorganic research which we were using as teaching exercises, while others produced output which was much below the standard which we aspired to.  We found none which would both cope with the load of class teaching and produce excellent output for the chemistry which we wanted to teach.

Clearly the solution was to produce a stand-alone program which would run in the students' PCs, rather than a server-side web-based program.  The author had written a Basic version of PAT in 1974, which he translated to Pascal in 1985.  A version in Prospero Pascal for DOS, in 1993, added peak labelling somewhat similar to the present version, but the program was still conversational and could display only one pattern at a time.  In 1999, the ProPascal version became unusable because of purchase of PCs with non-compatible graphics adapters.  The author therefore determined to produce a Windows based version, using Salford ClearWin+ Fortran 90.  The newer features of Fortran allowed direct translation of pointer-based lists used in the 1985 Pascal version for dynamic memory management, which give the program its flexibility.

Platforms

Availability

Built-in Help

Introduction
Using PAT
Setup
The Elements File

Introduction

• PAT was written originally for use in research, to enable the identification of fragment ions of chlorocarbon derivatives according to their chlorine isotope patterns in low resolution mass spectra.  It has been used also in work on polynuclear metal compounds, to find the number of metal atoms in fragments, and on phosphorus selenide fragments, to find the number of selenium atoms
• PAT may be used as a learning tool in a taught drylab environment, to aid understanding of mass spectroscopy
• Students may be provided with plots of experimental low resolution mass spectra.  They run PAT to predict isotope patterns for different numbers of atoms of elements which have several naturally abundant isotopes, and by matching these against the patterns in the provided spectra, identify the ions responsible for the various clusters of peaks
• PAT opens separate windows for up to 20 patterns at a time, so that alternative assignments may be compared with an experimental spectrum
• The patterns are for a low resolution spectrum, i.e. peaks are assumed to be at integer mass numbers
• Intensities at each mass are simply summed, without regard to mass deficiency of isotopes, which at high resolution makes different combinations of isotopes at the same mass number appear at slightly different mass, and perhaps be resolved from each other
• The error in peak height from assuming perfect alignment is not significant, and experimental low resolution patterns are easily recognised with the aid of PAT
• Only for an ion containing a large number of atoms of isotopes with large mass deficiencies might the high resolution mass round to the next mass number, making the mass numbers displayed by PAT be wrong by one mass unit.  In practical use of PAT, the author is not aware of any cases where this has happened
• Modern high resolution mass spectrometers include software to fit the high resolution mass of peaks, enabling certain identification of fragment ions in many cases. However, the amount of data involved is large, and it is often quicker to identify isotope patterns visually with the aid of PAT, before obtaining confirmation from the high resolution masses of particular peaks

Using PAT

• To calculate an isotope pattern, block over or delete the provided demonstration formula C Cl 3, and type the formula of the ion in the Formula box.  Either press Enter, or click the Calculate button
• Formulae consist of element symbols and numbers of atoms, all separated by one or more spaces
• If the number of atoms is 1, it may be omitted, as in a normal chemical formula
• The element symbols are not case sensitive:  thus, Cl CL cl (or cL) are all valid symbols for chlorine
• What you type will appear in the title bar of the resulting pattern window, just as you type it, providing PAT recognises it as a valid formula
• Because the case requirements of a normal chemical formula have been relaxed in the interest of easier typing, spaces are necessary between the symbols, even between an element symbol and number of atoms:  thus, C Cl3 is not valid, and will raise the error message 'Element CL3  is not in the data file'.  If this happens, click OK and insert the required space(s) in the formula, and try again
• No group symbols such as Me have been provided:  only element symbols are allowed, when using the provided isotope file ISTOP.EXT
• Parentheses or brackets are not allowed
• PAT will accept formulae containing up to 10 elements, which is far beyond what is normally encountered
• For each valid formula entered, PAT will open a separate window showing the calculated isotope pattern
• The window contains a scrollable list on the left.  The first column contains mass numbers of  peaks, and the second contains their relative intensities, with the largest normalised to 1000
• Leading or trailing peaks with less than 1/1000 of the height of the tallest peak, are omitted
• In the right side of the window is a line plot of the pattern, with vertical lines representing peaks, and the horizontal axis representing mass number
• Descending ticks are provided on the mass axis, at intervals of 1, 2 or 5 mass units, and two of these are labelled
• For most patterns, between one and five of the prominent peaks have mass number labels above them, to aid identification.

The molecular ion P 2 Se 5 provides an example of a fully labelled pattern, while for Se 7 the labels would be too crowded, so only the strongest peak is labelled
• In the present version of PAT, no printing facilities are provided:  the program is meant to be used interactively, and the results assessed on the screen
• PAT presents its pattern windows in stacks of five.  To navigate between them easily, use the drop-down list box at the right end of the tool bar, which shows the formulae for which windows are currently present
• If you try to generate more than 20 windows, the earliest in the drop down list will be progressively deleted
• You may also delete particular windows, to make space, by selecting them and then clicking their close button.  The drop-down list will be updated automatically, and you will be returned to the most recently created window

Setup

The screen resolution should be set to at least 800 by 600 pixels in Settings, Control Panel, Display. If the windows run off the bottom of your screen, you probably have the resolution set to 640 by 480.

If you install this program in a different PC, the library files SALFLIBC.DLL and FTN90.DLL need to be in the windows path or in the directory in which PATW is started. These libraries are commercial products, but you are permitted to take copies of them without charge.

The provided file of isotope data ISTOP.EXT should be in the directory in which PATW is started. Alternatively, you may provide a customised file of data for elements of interest to you, in the same format, and give its name as a parameter in the command line in which you run PATW from DOS, or separated by a space from the program name in the Target field of a shortcut which you create to run PATW from your desktop.

Introduction
Using PAT

The Elements File

Introduction

• PAT reads the relative abundances of natural isotopes of elements, from a file, into memory, when it starts up, thus speeding its subsequent use
• Because the total number of natural isotopes of all known elements is very large, it is intended that the data file should contain only those of possible interest to the user, and should be customised to particular uses of PAT
• By default, PAT reads a data file called ISTOP.EXT from the directory (folder) in which it is started
• Alternatively, a file, in the same format, but with any name, may be specified in the command line which runs PAT
• This file need not be in the start up directory, if its full path is given
• A specified file will be read in preference to ISTOP.EXT, if both are present in the start up directory

Making a Customised Data File

• A customised data file may be created by copying the supplied ISTOP.EXT and altering the copy with a text editor such as Notepad
• Only ASCII (DOS) text should be present in the file:  beware of word processors such as Word
• The first two characters of the first line of the file are the number of elements in the file
• This is followed for each element by:
• The one or two character element symbol as the first and only two characters of a line
• A line containing the isotope data for the element
• The isotope data line starts with the number of isotopes, followed by, with all numbers separated by one or more spaces, a pair of numbers for each isotope
• For each isotope, the first member of the pair of numbers is its mass number (i.e. an integer) and the second is its percentage natural abundance, which must be given including a decimal point
• Up to 10 isotopes are allowed per element
• Isotopes with abundance of less than 0.1% may be omitted

Group Abbreviations in a Customised Data File

• It is possible, if desired, to customise PAT to accept two-character group abbreviations such as Me, Ph or Bz, by entering them in a customised data file as elements
• PAT is case insensitive, so you cannot use capitalisation to distinguish between groups
• PAT may be used to find the isotope pattern for the group.  Normalise the relative intensities of the significant peaks to percentages, and enter them in the file as abundances of 'isotopes' having the mass numbers of the peaks

Installation

No further installation under Windows is required.  The software may be uninstalled simply by deleting patw.exe and the two .dll files.

Disclaimer

The author makes no commitment to remedy reported bugs or make suggested improvements, but nevertheless would welcome comments from users.
  They should be sent to:
  Bruce.Tattershall@ncl.ac.uk
 

Feedback

Thanks very much.

Bruce Tattershall
School of Chemistry
University of Newcastle
Newcastle upon Tyne
England

Email:       Bruce.Tattershall@ncl.ac.uk
Website:   http://www.staff.ncl.ac.uk/bruce.tattershall/