Specialize 1.0 – Identification of Peptides with complex PTM from Tandem Mass Spectra

Specialize 1.0

:: DESCRIPTION

Specialize is a novel approach to enable the expedited development of new algorithms for any types of PTM (post-translational modifications) peptide fragmentation.

::DEVELOPER

CCMS The Center for Computational Mass Spectrometry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 Specialize

:: MORE INFORMATION

Citation

A Turn-key Approach for Large-scale Identification of Complex Post-translational Modifications
Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne PE, Bandeira N. J
Proteome Res. 2014 Mar 7;13(3):1190-9. doi: 10.1021/pr400368u. Epub 2014 Jan 29.

Peptides 2.6 – Peptide and Protein Physico-chemical Properties

Peptides 2.6

:: DESCRIPTION

Peptides is a program for calculation of peptide/protein parameters from a given sequence. It calculates number of residues, molecular mass, the molecular formula, volume, pI, amino acid content and a pH-charge correlation (‘titration curve’).

::DEVELOPER

Hofmann Laboratory, Eskitis Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 Peptides

 :: MORE INFORMATION

Citation

Hofmann, A., Wlodawer, A. (2002)
PCSB – a programme collection for structural biology and biophysical chemistry.
Bioinformatics 18, 209-210.

PepSurf 3.0 / Mapitope 20070210 – Epitope Mapping using Affinity-selected Peptides

PepSurf 3.0 / Mapitope 20070210

:: DESCRIPTION

PepSurf is a program for mapping a set of peptides, affinity selected against a probe molecule, onto a three dimensional structure of a target protein.

The Mapitope algorithm is based on the underlying assumption that the entire set of peptides is enriched with amino-acid pairs which mimic the epitope.

DEVELOPER

Department of Cell Research and Immunology, Tel Aviv University,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  PepSurf  / Mapitope

:: MORE INFORMATION

Citation

Mayrose I, Penn O, Erez E, Rubinstein ND, Shlomi T, Tarnovitski Freund N, Bublil E, Rupin E, Sharan R, Gershoni JM, Martz E, Pupko T. 2007.
Pepitope: epitope mapping from affinity-selected peptides.
Bioinformatics 23(23):3244-3246.

Bublil EM, Freund NT, Mayrose I, Penn O, Roitburd-Berman A, Rubinstein ND, Pupko T, Gershoni JM. 2007.
Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm.
Proteins. 68(1):294-304

MALDIPepQuant 3.1 – Quantify MALDI peptides (SILAC) from Phenyx output

MALDIPepQuant 3.1

:: DESCRIPTION

MALDIPepQuant is a tool to quantify MALDI peptides (SILAC) from Phenyx  output

::DEVELOPER

Swiss Institute of Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • Java

:: DOWNLOAD

 MALDIPepQuant

:: MORE INFORMATION

Citation

Coute Y., Hernandez C., Appel R. D., Sanchez J.-C., Margolles A. 2007.
Labeling of Bifidobacterium longum Cells with 13C-Substituted Leucine for Quantitative Proteomic Analyses.
Appl. Environ. Microbiol. 2007 Sep;73(17):5653-6. Epub 2007 Jun 29