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.
We will be making the program available for download as soon as we have ironed out some remaining GUI bugs. Please visit back soon.
While the physical principles behind drift cell ion mobility mass spectrometry (IMMS) 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.
How to use the spreadsheet
- Mason, E. A.; McDaniel, E. W. Transport Properties of Ions in Gases; Wiley: New York, 1988.
- Wildgoose JL; Giles K; Pringle S; Koeniger S; Valentine S; Bateman RH; Clemmer D. 2006 53rd ASMS Conference on Mass Spectrometry & Allied Topics Seattle.
- 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.
- Ruotolo, B. T.; Benesch, J. L.; Sandercock, A. M.; Hyung, S. J.; Robinson, C. V. Nat. Protoc. 2008, 3, 1139-1152.
- Williams, J. P.; Scrivens, J. H. Rapid Commun. Mass Spectrom. 2008, 22, 187-196.
- Thalassinos, K., Grabenauer, M., Slade, S. E., Hilton, G. R., Bowers, M. T. and Scrivens, J. H. (In press) Anal. Chem.
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
This program is freely distributed. Use at your own risk.
Requirements: Java Runtime Environment v1.4.2 or later.
Download: Please email Kostas Thalassinos to obtain a copy. Once downaloaded 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.
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.