Phobius is "a combined transmembrane topology and signal peptide predictor". 


Trinotate is a transcriptome annotation suite designed for use with de novo assembled transcriptomes from model or non model organisms.


TMHMM is software for the prediction of transmembrane helices in proteins.


To use this program at MSI, please send a a request to and ask to be added to the TMHMM group. The use of TMHMM at MSI is limited to academic researchers.


The ProteoWizard Library and Tools are a set of modular and extensible open-source, cross-platform tools and software libraries that facilitate proteomics data analysis.

The libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations.


CD-HIT is a program for clustering large protein database at high sequence identity threshold. The program removes redundant sequences and generate a database of only the representatives. It can be applied in protein family classification, domain analysis, organizing large protein databases, improving performance of database search, and much more.


ProteinPilot™ Software can perform protein identification and quantitation, along with prediction of hundreds of peptide modifications and non-tryptic cleavages simultaneously. The protein grouping algorithm helps in distinguishing protein isoforms and visualize peptide-protein associations and relationships. The new version can take in generic input for non-AB SCIEX instruments via .mgf format.

X! Tandem

X! Tandem is open source software that can match tandem mass spectra with peptide sequences. X! tandem generates theoretical spectra for peptide sequences using information about intensity associated with amino acids. These spectra are compared with experimental data to generate an expectation value as a threshold score.

InterProscan - Protein Motif Search Tools

InterProScan software combines several protein motifs/domains search tools together. It allows users to scan protein sequences at one time against several signature databases including Prosite, PRINTS, PFAM, P roDom, Smart, TIGRFAMs, SignlP, Trans memberane etc., and also gives GO annotation.