PROMPT: Protein Mapping and Comparison Tool

PROMPT is a platform independent system for retrieval, analysis, mapping and comparison of protein sets. It allows easy mapping of different types of sequence identifiers, automatical data retrieval and integration, a multitude of analysis and comparison algorithms and a full-featured easy to use graphical user interface (GUI) application with an integrated help-system. Moreover exhaustive statistical tests are conducted in appropriate cases automatically or could be performed manually. Furthermore all analysis results can be viewed or visualized with one mouse-click and exported in various formats e.g. to Microsoft Excel. Additionally all methods can be used easily in your own Java code or with powerful beanshell scripting in own scripts, a pipeline or grid systems.

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Case Studies


PROMPT reference

Schmidt, T., Frishman, D. (2006), PROMPT: a protein mapping and comparison tool,
BMC Bioinformatics 2006, 7:331; Link

Publications that cite PROMPT

Coupling a Detergent Lysis/Cleanup Methodology with Intact Protein Fractionation for Enhanced Proteome Characterization
Sharma, R et al.
J. PROTEOME RES. 2012, 11 (12), pp 6008 - 6018
DOI: 10.1021/pr300709k

Bacterial protein structures reveal phylum dependent divergence.
Shortridge, MD et al.
COMPUT. BIOL. CHEM.2011 Feb;35(1):24-33.
DOI: 10.1016/j.compbiolchem.2010.12.004

Probing the Phosphoproteome of HeLa Cells Using Nanocast Metal Oxide Microspheres for Phosphopeptide Enrichment
Leitner, A et al.
ANALYTICAL CHEMISTRY, 82 (7): 2726-2733 APR 1 2010
DOI: 10.1021/ac902560z

Helicobacter pylori proteomics by 2-DE/MS, 1-DE-LC/MS and functional data mining
Jungblut, PR et al.
PROTEOMICS, 10 (2): 182-193 JAN 2010
DOI: 10.1002/pmic.200900361

Urinary Proteomics Evaluation in Interstitial Cystitis/Painful Bladder Syndrome: A Pilot Study
Tseng, LH (Tseng, Ling-Hong)

Differential substrate specificity of group I and group II chaperonins in the archaeon Methanosarcina mazei
Hirtreiter, AM et al.
MOLECULAR MICROBIOLOGY, 74 (5): 1152-1168 DEC 2009
DOI: 10.1111/j.1365-2958.2009.06924.x

Sequence-Based Prediction of Type III Secreted Proteins
Arnold, R et al.
PLOS PATHOGENS, 5 (4): Art. No. e1000376 APR 2009
DOI: 10.1371/journal.ppat.1000376

Protein abundance profiling of the Escherichia coli cytosol
Ishihama Y, Schmidt T, Rappsilber J, et al.
BMC GENOMICS Volume: 9 Article Number: 102 Published: FEB 27 2008
DOI: 10.1186/gb-2008-9-6-r104

An evolutionary and structural characterization of mammalian protein complex organization
Wong, P et al.
BMC GENOMICS, 9: Art. No. 629 DEC 23 2008
DOI: 10.1186/1471-2164-9-629

OREST - Online resource for EST analysis
Wägele B, Schmidt T, Ruepp A, Mewes HW
NUCLEIC ACIDS RESEARCH, 36: W140-W144 Suppl. S JUL 2008
DOI: 10.1093/nar/gkn253

An approach to handling and interpretation of ambiguous data in transcriptome and proteome comparisons
Irmler M, Hartl D, Schmidt T, et al.
PROTEOMICS, 8 (6): 1165-1169 MAR 2008
DOI: 10.1002/pmic.200700741

The fungus Ustilago maydis and humans share disease-related proteins that are not found in Saccharomyces cerevisiae
Munsterkotter M, Steinberg G
BMC GENOMICS, 8: Art. No. 473 DEC 20 2007
DOI: 10.1186/1471-2164-8-473

Assignment of isochores for all completely sequenced vertebrate genomes using a consensus
Schmidt, T; Frishman, D
GENOME BIOLOGY, 9 (6): Art. No. R104 2008
DOI: 10.1186/gb-2008-9-6-r104

SIMAPstructuring the network of protein similarities
Rattei T, Tischler P, Arnold R, et al.
NUCLEIC ACIDS RESEARCH Volume: 36 Special Issue: Sp. Iss. SI Pages: D289-D292 Published: JAN 2008
DOI: 10.1093/nar/gkm963

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases
Cote RG, Jones P, Martens L, et al.
BMC BIOINFORMATICS Volume: 8 Article Number: 401 Published: OCT 18 2007
DOI: 10.1186/1471-2105-8-401

Bioinformatics for study of autoimmunity.
Petrovsky N, Brusic V.
AUTOIMMUNITY. 2006 Dec;39(8):635-43.

PEDANT genome database: 10 years online.
Riley ML, Schmidt T, Artamonova II, Wagner C, Volz A, Heumann K, Mewes HW, Frishman D.
DOI: 10.1093/nar/gkl1005

DnaK Functions as a Central Hub in the E. coli Chaperone Network.
Chen Taotao
Dissertation, LMU Muenchen: Faculty of Chemistry and Pharmacy 12. December 2011

Development and application of computational methdologies for Integrated Molecular Systems Biology
Karathia, Hiren Mahendrabhai
PhD thesis, Universitat de Lleida. Departament de Ciencies Mediques Basiques 2012-11-30

TOOLbox - PROMPT for comparisons,
Vol. 5, No. 9: September 2006; pp 2072–2073;
Web-version, PDF-screen, PDF-print, About the journal