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.
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 – the 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