Challenger

Challenger is a web application that enables the processing of collision induced unfolding (CIU) ion mobility data. The program automatically creates CIU fingerprints and summary plots that capture the increase in collision cross section and the increase in conformational flexibility of proteins during unfolding.

The input data is a tab delimited file with the following format
WT-CIU45V 50V 55V 60V
5.760.0000.000.000
5.940.0000.000.000
6.120.0000.000.000
6.30.2000.000.000
6.485.9901.710.020
6.6626.6714.732.970.05
6.8457.0038.5315.631.07
7.0284.5368.8138.567.79
...
where the first column contains the name of the experiment followed by the ATD (or CCS) values and each subsequent row representing one ATD for each voltage

The program is written in JavaScript and runs in the web browser you use to access the site. No transmission of your data takes place to our servers, it remains in your own computer.

This program is freely distributed. Use at your own risk.

Run Challenger WebApp

challenger 

Reference: The program has been described in the following publication. Please reference if you use the program in your own work.

Sivalingam, G.N., Cryar, A., Williams, M.A, Gooptu, B., Thalassinos, K. (Under Review) Deconvolution of ion mobility mass spectrometry arrival time distributions using a genetic algorithm approach: application to α1-antitrypsin peptide binding.

Amphitrite

Amphitrite is a software package that enables the processing of T-Wave ion mobility data. The program can deconvolute components in a mass spectrum and uses this information to extract corresponding arrival time distributions (ATDs) with minimal user intervention. It can also be used to automatically create a collision cross section (CCS) calibration and apply this to subsequent files of interest.

Mass spectrum deconvolution can be performed (with AtroposGui.exe) using text files and so is compatible with data from all mass spectrometers. The ion mobility functionality, however, currently only works with Synapt G1 data, but we hope to extend this to G2(s) data. You can download the program and some sample data from the following links. The program is distributed using the GNU General Public License, version 2. Please read the GNU licence and the README.txt file.

This program is freely distributed. Use at your own risk.

Amphitrite Program (Windows 64 bit)
Sample data

The source code for the software package is available as a GitHub repository as well.

Amphitrite GitHub

amphitrite 

Reference: The program has been described in the following publication. Please reference if you use the program in your own work.

Sivalingam, G.N., Yan, J., Sahota, H., Thalassinos, K. (2013) Amphitrite: a program for processing travelling wave ion mobility data. International Journal of Mass Spectrometry. 345, 54–62.

Synapt Calibration

While the physical principles behind drift cell ion mobility mass spectrometry (IM-MS) are well understood1 and can be used to obtain a collision cross-section for each ion studied, the same is not true for the T-Wave based device. Methods to create a cross-sectional calibration for the Synapt have been previously published2-5. The approach our group has developed is a modified version of Wildgoose et al.2. An excel spreadsheet used to simplify the creation and use of a cross-sectional calibration is made available here. A description of our approach is presented in Thalassinos et al.6. If you use this spreadsheet please reference the following paper:

Thalassinos, K., Grabenauer, M., Slade, S. E., Hilton, G. R., Bowers, M. T. and Scrivens, J. H. (2009) Characterisation of phosphorylated peptides using travelling wave-based and drift cell ion mobility mass spectrometry. Analytical Chemistry 81:248-254.

Excel spreadsheet
How to use the spreadsheet

  1. Mason, E. A.; McDaniel, E. W. Transport Properties of Ions in Gases; Wiley: New York, 1988.
  2. Wildgoose JL; Giles K; Pringle S; Koeniger S; Valentine S; Bateman RH; Clemmer D. 2006 53rd ASMS Conference on Mass Spectrometry & Allied Topics Seattle.
  3. Scrivens, J. H.; Thalassinos, K.; Hilton, G. R.; Slade, S. E.; Pinherio, T. J. T.; Bateman, R. H.; Grabenauer, M.; Bowers, M. T. 2007. 54th ASMS Conference on Mass Spectrometry & Allied Topics.
  4. Ruotolo, B. T.; Benesch, J. L.; Sandercock, A. M.; Hyung, S. J.; Robinson, C. V. Nat. Protoc. 2008, 3, 1139-1152.
  5. Williams, J. P.; Scrivens, J. H. Rapid Commun. Mass Spectrom. 2008, 22, 187-196.
  6. Thalassinos, K., Grabenauer, M., Slade, S. E., Hilton, G. R., Bowers, M. T. and Scrivens, J. H. (2009) Characterisation of phosphorylated peptides using travelling wave-based and drift cell ion mobility mass spectrometry. Analytical Chemistry 81:248-254.

Polymerator

Polymerator is a program that aids the interpretation of tandem mass spectrometry (MS/MS) data from synthetic polymers. The software is particularly focused toward aiding the end-group determination of these materials by significantly speeding up the interpretation process. This allows information on the initiator and/or chain transfer agents, used to generate the polymer, and the mechanism of termination to be inferred from the data much more rapidly. The software allows the validity of hypothesized structures to be rapidly tested by automatically annotating the data file using previously proposed fragmentation rules for synthetic polymers.

This program is freely distributed. Use at your own risk.

Requirements: Java Runtime Environment v1.4.2 or later.

Download: Once downloaded extract the zip file and then double click on the Polymerator-v1.2.jar file in order to start the program.

Reference: The program has been described in the following publication. Please reference if you use the program in your own work.

Thalassinos, K., Jackson, A. T., Williams, J. P., Hilton, G. R., Slade, S. E. and Scrivens, J. H. (2007). Novel software for the assignment of peaks from tandem mass spectrometry spectra of synthetic polymers. Journal of the American Society for Mass Spectrometry 18: 1324-1331.

trypsin 
Other publications where polymerator has been used are:

Jackson, A. T., Slade, S. E., Thalassinos, K. and Scrivens, J. H. (2008). End group characterisation of poly(propylene glycol)s by means of electrospray ionisation-tandem mass spectrometry (ESI-MS/MS). Analytical and Bioanalytical Chemistry 392: 643-650.

Williams, J. P., Hilton, G. R., Thalassinos, K., Jackson, A. T. and Scrivens, J. H. (2007). The rapid characterisation of poly(ethylene glycol) oligomers using desorption electrospray ionisation tandem mass spectrometry combined with novel product ion peak assignment software. Rapid Communications in Mass Spectrometry 21: 1693-1704.

Native Mass Spectrometry Calculator

A resource used during native and ion mobility mass spectrometry experiments. Provides access to common calculations e.g. calculation of theoretical charge states from mass, mass from m/z values etc.

MS Calculations

Concentration Calculations