Web online resources:

RAId
Robust Accurate Identification - a suite of proteomics tools
MIDAs
Molecule's Isotopic Distribution Analysis
ITM Probe
Information Transduction Module
SaddleSum
Robust and accurate data enrichment statistics via distribution function of sum of weights
DeCoaD
Determining correlations among diseases using protein interaction networks
LogOddsLogo
Sequence logos generation from biological sequence alignments