The Epithelial Systems Biology Laboratory, headed by Mark Knepper, has developed a number of computational tools for analysis of proteomic data and have made them available to the community. The following links allow users to access online versions of the tools or download executables:

AbDesigner - a tool for choosing peptide sequences from specific proteins that are immunogenic, unique, and lacking in post-translational modifications.
Automated Bioinformatics Extractor (ABE) - a batch tool for extraction of specified information about specific proteins from UniProt or RefSeq protein records.
Conditional Allele Mouse Planner (CAMP) - a tool for designing protocols for breeding transgenic and knockout mice with cost estimation.
CPhos - information theory-based algorithm to assess the conservation of phosphorylation sites among species.
NGS-Integrator - a tool for combining multiple NGS data tracks into a single track using Bayesian methods.
PhosphoLogo - a tool for generating information-based sequence logos from a list of equal-length peptide sequences surrounding a phosphorylated residue.
PTMLogo - an improved tool for generating information-based sequence logos from a list of equal-length peptide sequences surrounding a phosphorylated residue (Uses position-specific background).
ProMatch - a program to match peptide and mRNA sequences to entries in NCBI Reference Sequence Database (RefSeq).
PTM Centralizer - converts MS-identified peptides containing a specific feature (e.g. a phosphorylation site) to a sequence of given length with the feature in the center.
Renal Inner Medulla Free-Energy Calculator - a tool for calculation of net free energy change in steady-state models of the renal concentrating mechanism.
virtualBlot - a program for predicting location of bands on immunoblots based on protein mass spectrometry data from sliced SDS-PAGE gels.
Temporal Pattern Mining (TPM)algorithm - clusters time-series data sets according to time-course pattern.