ProteinLasso – Lasso Regression Approach to Protein Inference problem

ProteinLasso

:: DESCRIPTION

The new inference algorithm ProteinLasso explores an ensemble learning strategy to address the sparsity parameter selection problem in Lasso model.

::DEVELOPER

ProteinLasso team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux / Windows
  • JRE

:: DOWNLOAD

   ProteinLasso

:: MORE INFORMATION

Citation

Comput Biol Chem. 2013 Apr;43:46-54. doi: 10.1016/j.compbiolchem.2012.12.008. Epub 2013 Jan 12.
ProteinLasso: A Lasso regression approach to protein inference problem in shotgun proteomics.
Huang T1, Gong H, Yang C, He Z.

ProteinInfer – A Combinatorial Perspective of the Protein Inference Problem

ProteinInfer

:: DESCRIPTION

ProteinInfer is a softwarr for combinatorial perspective of the protein inference problem

::DEVELOPER

Laboratory for Bioinformatics and Computational Biology, HKUST

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ProteinInfer

:: MORE INFORMATION

Citation:

A combinatorial perspective of the protein inference problem.
Yang C, He Z, Yu W.
IEEE/ACM Trans Comput Biol Bioinform. 2013 Nov-Dec;10(6):1542-7. doi: 10.1109/TCBB.2013.110.

ProteinART – Protein Inference solutions from Proteome ARTworks

ProteinART

:: DESCRIPTION

ProteinART is a web tool that uses combinatorial optimization for protein inference from tandem mass spectrometry peptide identifications. It uses a set of confidently identified peptides, peptide detectability, and a protein database to provide the most likely set of identified proteins.

::DEVELOPER

Haixu Tang, Predrag Radivojac

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Pac Symp Biocomput. 2007:409-20.
Advancement in protein inference from shotgun proteomics using peptide detectability.
Alves P1, Arnold RJ, Novotny MV, Radivojac P, Reilly JP, Tang H.

MSBayesPro – Bayesian Protein Inference for LC-MS/MS Proteomics experiment

MSBayesPro

:: DESCRIPTION

MSBayesPro is a software package and web tool for Bayesian protein inference from tandem mass spectrometry peptide identifications. It uses a set of identified peptides (or peptides with scores in a MS/MS search), peptide detectability, and a protein database to provide probabilities of protein identifications.

::DEVELOPER

Yong Fuga Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 MSBayesPro

:: MORE INFORMATION

Citation

J Comput Biol. 2009 Aug;16(8):1183-93. doi: 10.1089/cmb.2009.0018.
A bayesian approach to protein inference problem in shotgun proteomics.
Li YF1, Arnold RJ, Li Y, Radivojac P, Sheng Q, Tang H.

PAnalyzer 1.1 – Protein Inference in Shotgun Proteomics

PAnalyzer 1.1

:: DESCRIPTION

PAnalyzer is a software tool focused on the protein inference process of shotgun proteomics.

::DEVELOPER

EhuBio

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX

:: DOWNLOAD

 PAnalyzer

:: MORE INFORMATION

Citation:

Prieto G, Aloria K, Osinalde N, Fullaondo A, Arizmendi JM, Matthiesen R:
PAnalyzer: A software tool for protein inference in shotgun proteomics.
BMC bioinformatics 2012, 13:288.