@article{yang_ramidssoon_hamlett_giddings_2008, title={High-accuracy peptide mass fingerprinting using peak intensity data with machine learning}, volume={7}, ISSN={["1535-3893"]}, DOI={10.1021/pr070088g}, abstractNote={For MALDI-TOF mass spectrometry, we show that the intensity of a peptide-ion peak is directly correlated with its sequence, with the residues M, H, P, R, and L having the most substantial effect on ionization. We developed a machine learning approach that exploits this relationship to significantly improve peptide mass fingerprint (PMF) accuracy based on training data sets from both true-positive and false-positive PMF searches. The model's cross-validated accuracy in distinguishing real versus false-positive database search results is 91%, rivaling the accuracy of MS/MS-based protein identification.}, number={1}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Yang, Dongmei and Ramidssoon, Kevin and Hamlett, Eric and Giddings, Morgan C.}, year={2008}, month={Jan}, pages={62–69} }
 @article{khatun_ramkissoon_giddings_2007, title={Fragmentation characteristics of collision-induced dissociation in MALDI TOF/TOF mass spectrometry}, volume={79}, ISSN={["0003-2700"]}, DOI={10.1021/ac061455v}, abstractNote={The identification of proteins by tandem mass spectrometry relies on knowledge of the products produced by collision-induced dissociation of peptide ions. Most previous work has focused on fragmentation statistics for ion trap systems. We analyzed fragmentation in MALDI TOF/TOF mass spectrometry, collecting statistics using a curated set of 2459 MS/MS spectra and applying bootstrap resampling to assess confidence intervals. We calculated the frequency of 18 product ion types, the correlation between both mass and intensity with ion type, the dependence of amide bond breakage on the residues surrounding the cleavage site, and the dependence of product ion detection on residues not adjacent to the cleavage site. The most frequently observed were internal ions, followed by y ions. A strong correlation between ion type and the mass and intensity of its peak was observed, with b and y ions producing the most intense and highest mass peaks. The amino acids P, W, D, and R had a strong effect on amide bond cleavage when situated next to the breakage site, whereas residues including I, K, and H had a strong effect on product ion observation when located in the peptide but not adjacent to the cleavage site, a novel observation.}, number={8}, journal={ANALYTICAL CHEMISTRY}, author={Khatun, Jainab and Ramkissoon, Kevin and Giddings, Morgan C.}, year={2007}, month={Apr}, pages={3032–3040} }
 @article{su_hutchison_giddings_2007, title={Mapping phosphoproteins in Mycoplasma genitalium and Mycoplasma pneumoniae}, volume={7}, journal={BMC Microbiology}, author={Su, H. C. and Hutchison, C. A. and Giddings, M. C.}, year={2007} }