Proteome Signatures How Are They Obtained and What Do They Teach Us?

Supplementary data

Proteome signatures – how are they obtained and what do they teach us?

AppliedMicrobiologyandBiotechnology

João Pinto da Costa, Virginia Carvalhais, Rita Ferreira, Francisco Amado,Manuel Vilanova, Nuno Cercaand Rui Vitorino

* Corresponding author:

Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal

Table S1: Available commercial and open-source tools for 2D gel analysis.

License / Software / Company/Developer / Ref.
Commercial / PDQuest / BioRad / (BioRad 2015)
Delta2D / Decodon / (Decodon 2015)
ImageMaster2D / GE Healthcare / (GE-Healthcare 2015)
BioNumerics 2D / AppliedMaths / (AppliedMaths 2015)
Melanie / GeneBio / (GeneBio 2015)
REDFIN / Ludesi / (Ludesi 2015)
Open-source/Freeware / Gel2DE / Van Belle et al. / (Van Belle et al. 2006)
GelScape / University of Alberta / (Young and Wishart 2015)
Melanie Viewer / Swiss Institute of Bioinformatics / (SIB 2015)

Table S2:Proteomics-related bioinformatics resources. These are categorized according to their main feature/goal.

Category / Resource / Purpose/Feature / Ref.
Databases / Protein Data Bank / Repository of 3D structures / (Berman et al. 2000)
UniProtKB / Functional information / (Catherman et al. 2013)
STRING / Protein-protein interactions / (Franceschini et al. 2013)
Swiss-MODEL / Protein structure homology models / (Kiefer et al. 2009)
PROSITE / Protein domains, functional sites and families / (Sigrist et al. 2013)
neXtProt / Integrated database of Human proteins / (Bridge et al. 2014)
Tools* / BLAST, BLAST-NCBI, BLAST-PBIL / Sequence similarity search / (Morgulis et al. 2008)
DisEMBL / Prediction of disordered protein regions / (Linding et al. 2003)
AACompldent, AAComplSim / Aminoacid composition comparison / (Wilkins et al. 1999)
HeliQuest / Alpha-helical properties screening / (Gautier et al. 2008)
ALF / Genome evolution simulation / (Dalquen et al. 2012)
CPHModels / Protein homology modelling / (Nielsen et al. 2010)
CFSSP / Secondary structure prediction / (Chou and Fasman 1974)
ClustalW / Multiple sequence alignment / (Thompson et al. 1994)
Compute pI/Mw / Computation of isolelectric point (pI) and molecular weight (Mw) / (Gasteiger et al. 2005)
InsPecT / MS/MS tool to identify modified peptides / (Frank et al. 2005)
PDBePISA / Proteins, interfaces, surfaces and assemblies / (Krissinel 2010)
TargetP / Subcellular location prediction / (Emanuelsson et al. 2007)

*The herein presented tools are merely representative of the large number of Proteomics-related tools available online.

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