Tandem mass spe
ctrometry (MS/MS) te
chniques, developed for protein identifi
cation, are in
creasingly being applied in the field of peptidomi
cs. Using this approa
ch, the set of protein fragments observed in a sample of interest
can be determined to gain insights into important biologi
cal pro
cesses su
ch as signaling and other bioa
ctivities. As the peptidomi
cs era progresses, there is a need for robust and
convenient methods to inspe
ct and analyze MS/MS derived data. Here, we present Peptigram, a novel tool dedi
cated to the visualization and
comparison of peptides dete
cted by MS/MS. The prin
cipal advantage of Peptigram is that it provides visualizations at both the protein and peptide level, allowing users to simultaneously visualize the peptide distributions of one or more samples of interest, mapped to their parent proteins. In this way rapid
comparisons between samples
can be made in terms of their peptide
coverage and abundan
ce. Moreover, Peptigram integrates and displays key sequen
ce features from external databases and links with peptide analysis tools to offer the user a
comprehensive peptide dis
covery resour
ce. Here, we illustrate the use of Peptigram on a data set of milk hydrolysates. For
convenien
ce, Peptigram is implemented as a web appli
cation, and is freely available for a
cademi
c use at
cd.ie/peptigram" class="extLink">http://bioware.ucd.ie/peptigram.