Pipasic 20140121 – Protein Abundance Correction in Metaproteomic Data

Pipasic 20140121

:: DESCRIPTION

Pipasic (peptide intensity-weighted proteome abundance similarity correction) is a tool which corrects identification and spectral counting based quantification results using peptide similarity estimation and expression level weighting within a non-negative lasso framework.

::DEVELOPER

Bernhard Y. Renard

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ WIndows/ MacOsX
Python
BioPython

:: DOWNLOAD

Pipasic

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 15;30(12):i149-i156. doi: 10.1093/bioinformatics/btu267.
Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics.
Penzlin A, Lindner MS, Doellinger J, Dabrowski PW, Nitsche A, Renard BY

ALL-P – Including shared Peptides for Estimating Protein Abundances

ALL-P

:: DESCRIPTION

ALL-P is a statistical framework based on a hierarchical modeling that takes into account shared peptide information for estimating protein abundances. ALL-P performs a simultaneous analysis of all the quantified peptides, handling the biological and technical errors as well as the peptide effect.

::DEVELOPER

pappso (Plate-forme d’analyses protéomiques de Paris Sud-Ouest)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ MacOsX / Linux
R package

:: DOWNLOAD

ALL-P

:: MORE INFORMATION

Citation

Blein-Nicolas M., Xu H., de Vienne D., Giraud C., Huet S., Zivy, M. (2012)
Including shared peptides for estimating protein abundances: a significant improvement for quantitative proteomics.
Proteomics.12 2797–2801 .

PARE – Compare Protein Abundance and mRNA Expression data

PARE

:: DESCRIPTION

PARE (Protein Abundance and mRNA Expression) is a tool for comparing protein abundance and mRNA expression data. In addition to globally comparing the quantities of protein and mRNA, PARE allows users to select subsets of proteins for focused study (based on functional categories and complexes). Furthermore, it highlights correlation outliers, which are potentially worth further examination.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

PARE

:: MORE INFORMATION

Citation:

EZ Yu, AE Burba, M Gerstein (2007)
PARE: a tool for comparing protein abundance and mRNA expression data.
BMC Bioinformatics 8: 309.