This laboratory has developed a wide range of computer programs / software to advance our research which utilize or help interpret mass spectral datasets. Many have broader uses for the scientific community.


An algorithm to build phylogenetic trees from the masses of peptides produced from the proteolytic digestion of multiple proteins (or 2022 - the protein masses). The 2017-present version also calculates single point mutations from a pairwise comparison of the mass datasets and displays these on the tree.

Lun ATL, Swaminathan K, Wong JWH, Downard KM (2013) Mass Trees – A New Phylogenetic Approach and Algorithm to Chart Evolutionary History with Mass Spectrometry, Anal. Chem. 85: 5475-5482.


Akand EH, Downard KM (2017) Mutational Analysis Employing a Phylogenetic Mass Tree Approach in a Study of the Evolution of the Influenza Virus, Mol. Phylogen. Evol. 112: 209-217.


Mann C, Downard KM (2022) Analysis of Bacterial Biotyping Datasets with a Mass Based Phylonumerics Approach, Anal. Bioanal. Chem., 414: 3411- 3417.



FluShuffle and FluResort

Used to identify the origins of influenza viral proteins and the number of reassortment events


Lun ATL, Wong JWH, Downard KM (2012) FluShuffle and FluResort - New Algorithms to Identify Reassorted Strains of the Influenza Virus by Mass Spectrometry, BMC Bioinformatics 13: 208.




Facilties the phylogenetic classification of influenza virus from mass spectral data using a novel random resampling function (Z-score).


Ma S, Wong JWH, Downard KM (2015) A Novel Algorithm and Approach to Score and Visualize the Phylogeny of the Influenza Virus using Mass Spectrometry, Anal. Chim. Acta 895: 54-61.


An algorithm to automatically type and subtype the influenza virus from mass spectral data using signature peptide masses / biomarkers


Schwahn AB, Wong JWH, Downard KM (2010) FluTyper - An Algorithm for Automated Typing and Subtyping of the Influenza Virus from High Resolution Mass Spectral Data, BMC Bioinformatics, 11: 266.



ETISEQ - Elution Time Ion SEQuencing

Enables the automated conversion of concurrent peptide fragmentation data through a correlation of precursor and product ion elution profiles. 


Wong JWH, Schwahn AB, Downard KM (2009) ETISEQ - an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics, BMC Bioinformatics, 10: 244.

PROXIMO - PRotein Oxidation Interface MOdeller
Utilizes a geometric surface fitting routine to predict likely structures for protein complexes using data generated in RP-MS / protein footprinting experiments.


Gerega SK, Downard KM (2006) PROXIMO - A Docking New Algorithm to Model Protein Complexes Using Data from Radical Probe Mass Spectrometry, Bioinformatics, 22: 1702-1709.

FluAlign and FluGest
Introduces two algorithms for the identification of conserved peptide motifs or unique mass within influenza viral proteins that can be used as signatures to type, subtype and determine the lineage of viruses


Schwahn AB, Wong JW, Downard KM (2009) Subtyping of the influenza virus by high resolution mass spectrometry. Anal Chem. 81: 3500-3506.



PRISM - PRotein Interactions from the Spectra of Masses

An algorithm which compares two mass spectra and identifies differences in their masses and intensities

Ho JWK, Morrissey B, Downard KM (2007) A Computer Algorithm for the Identification of Protein Interactions from the Spectra of Masses (PRISM), J. Am. Soc. Mass Spectrom., 18, 563– 566.



COMPLX - COMposition of Protein-Ligand compleXes

An algorithm for identifying protein-ligand or other macromolecular complexes detected in electrospray mass spectra, even those of complex mixtures. It takes advantage of the appearance of multiply charged ions that are common to electrospray ionization.


Wong JW, Downard KM (2003) COMPLX: a computer algorithm for the detection of protein-ligand and other macromolecular complexes in mass spectra. J Mass Spectrom. 38: 573-581.


Wong JW, Downard KM (2005) Performance of the computer algorithm COMPLX for the detection of protein complexes in the mass spectra of simulated biological mixtures. J Mass Spectrom.  40: 1187-1196.



CRAM - Charge Ratio Analysis Method
A new method to identify the charge of ions in electrospray (ESI) mass spectra through a ratio of the m/z values of adjacent ions, that can also be applied to identify the charge carrying species and the extent of isotopic enrichment in high resolution (eg FT-ICR) data sets 


Maleknia SD, Downard KM (2005) Charge Ratio Analysis Method: Approach for the Deconvolution of Electrospray Mass Spectra, Anal. Chem., 77: 111-119.


Maleknia SD, Downard KM (2005) Charge ratio analysis method to interpret high resolution electrospray Fourier transform-ion cyclotron resonance mass spectra, Int. J. Mass Spectrom. 246, 1-9.


Maleknia SD, Green DC (2010) eCRAM computer algorithm for implementation of the charge ratio analysis method to deconvolute electrospray ionization mass spectra, Int. J. Mass Spectrom. 290: 1-8.