High level view of the MAE algorithm. High level view of the MAE algorithm. Elements within the dotted line represent those in MAE. Elements above this box represent the search components (MSPlus, Mascot, and Sequest) and the MassAnalyzer, which is used to calculate theoretical spectra for candidate peptides in the MSPlus output file. The three inputs to MAE include (i) the DTA file, listing the MH+ for the parent peptide based on the observed ion m/z and the assumed charge along with m/z and intensities of fragment ions after centroiding; (ii) the candidate peptide sequence(s) from the search result (obtained from the MSPlus.csv common data interface generated by in-house software); and (iii) the theoretical MS/MS spectrum generated by MassAnalyzer, listing m/z and intensity of predicted fragment ions for candidate peptide sequence(s). Three MAE outputs include (i) the simplified sDTA file, (ii) the summary file listing annotations of the major ions in the sDTA file, and (iii) the MAE scores (e.g. Sim, PIC, y − b/y + b, and IntFrag), which are written to the MSPlus file. Finally MAE evaluates whether the scores are above user input thresholds for acceptance and writes the outcome to the MSPlus file. The list of validated peptides is input into an in-house IsoformResolver program to produce a protein profile. Shaojun Sun et al. Mol Cell Proteomics 2007;6:1-17 © 2007 The American Society for Biochemistry and Molecular Biology