My major academic interests are Biological Mass Spectrometry and Bioinformatics, particularly the interface between the two. I’m also fascinated about mapping biological systems. One of the ways of doing this is with Mass Spectrometry.
I have ported some of the old programs I’ve written to this site and will add links to other I have written soon.
There are two little web based utilities that can help out in a pinch:
The following software was developed while I was working in the Bioanalytical Chemistry Group at the Ludwig Institute for Cancer Research (LICR) at University College London, UK. LICR closed the London site and moved to Oxford university shortly after I finished my PhD and the server hosting this software eventually disappeared.
UltraMassList
UltraMassList is a helper program that extracts and manipulates mass and intensity data from Bruker xml peak files.
It allows a user to generate a set of mass, or mass and intensity files in the parent directory of the Bruker data files saving the user from drilling down through the folders for each spectra. The data files are in a format suitable for database searching with ProteinProspector, Mascot or similar search engines.
The windows binary
Perl source code for Unix/Linux/Sun or Mac computers
CommonContam
CommonContam identifies and removes common contaminant masses in a related set of MALDI MS spectra.
It generates a list of all the masses found and then removes duplicates that are within the user defined mass tolerance range. The user then selects a cut-off value. All masses that have been found in that many files or more will be removed. A new set of cleaned data files are generated ready for database searching. For Bruker data use UltraMassList to generate files ready for CommonContam to process.
The windows binary.
Perl source code for Unix/Linux/Sun or Mac computers.
ProteomeXplorer
ProteomeXplorer is a useful tool in the theoretical analysis of whole proteomes.
In silico analysis of whole proteomes under different conditions can facilitate the exploration of novel proteomic experiment strategies and help to evaluate derivation methods based on the exploitation of the properties associated with amino acids, particularly uncommon ones such as tryptophan, methionine and histidine or a combination of them.
The windows binary.
Perl source code for Unix/Linux/Sun or Mac computers.
LCMALDIprocessor
LCMALDIprocessor processes the mass spectrometry data produced in a LC MALDI MS and MS/MS experiment. It currently supports MS data from the Bruker range of MALDI instruments but has only been tested with data from the Bruker Ultraflex. LCMALDIprocessor extracts the mass and intensities of all the MS data. It utilises the common contaminant algorithm and generates a list of all the masses found and then removes duplicates that are within the user defined mass tolerance range.
The windows binary.
Perl source code for Unix/Linux/Sun or Mac computers.
UltaSamplePlate
UltaSamplePlate generates sample tables suitable for the analysis LC fractions by the Bruker UltraFlex MALDI mass spectrometer. The sample tables are in tab delimited format and are used by Brukers flexcontrol acquisition.
The windows binary.
Perl source code for Unix/Linux/Sun or Mac computers.
PIGOK – Protein Interrogation of Gene Ontology and KEGG databases
PIGOK is a database that holds the pI, Molecular Weight, Codon Adaptation Index ,Species, Entrez Gene number, Gene Ontology and KEGG information for each protein entry. The database can be accessed directly on the web via a CGI. The database schema, sequence file processing scripts, CGI and command line example script have been made available as a package to researches that wish to setup and run a database server of their own. The format of various source files have changed over time so this package is now out of date but it will be revived in the near future and hosted on this site.
Perl source code for Linux computers.
If you find any bugs in the web applications or downloadable software please feel free to file a bug report. Contact me if you wish to collaborate on the development of software for Mass Spectrometry.