Proteomic Resources

Open source proteomic protocols

In-solution trypsin digest protocol #1

In-solution trypsin digest protocol #2

In-gel trypsin digest protocol

Useful Web Links

Protein Prospector – in silico digests, peptide fragmentation, isotope patterns and much more.

Peptide mass calculator

Peptigram -a user friendly web application for peptidomics data visualization. Developed by University College, Dublin.

Peptide calculators – molecular weight, extinction coefficient, net charge at neutral pH, iso-electric point, water solubility

Protein mass/molarity converter

ABRF – delta mass – a database of different mass shifts due to chemical modifications. Developed by Melbourne’s Ken Mitchelhill.

Protter – an open-source tool for visualization of proteoforms and interactive integration of annotated and predicted sequence features together with experimental proteomic evidence.

Proteomic Databases and Search Engines

NCBI protein – ┬áthe major US protein database

The European Bioinformatic Institute (EBI) – the major European protein database with improved data presentation

Phosphosite – the largest database of post-translational modifications

ProteomicsDB – the human proteome