Category: proteomics

TBnovo – De novo Protein Sequencing by combining Top-down and Bottom-up Mass Spectrometry

TBnovo

:: DESCRIPTION

TBNovo is a de novo protein sequencing software tool which combines both top down and bottom up tandem mass spectra.

::DEVELOPER

Xiaowen Liu ,CCMS The Center for Computational Mass Spectrometry

:: REQUIREMENTS

  • Linux/Windows
  • JRE

:: DOWNLOAD

 TBnovo

:: MORE INFORMATION

Citation

J Proteome Res. 2014 Jul 3;13(7):3241-8. doi: 10.1021/pr401300m. Epub 2014 Jun 18.
De novo protein sequencing by combining top-down and bottom-up tandem mass spectra.
Liu X1, Dekker LJ, Wu S, Vanduijn MM, Luider TM, Tolić N, Kou Q, Dvorkin M, Alexandrova S, Vyatkina K, Paša-Tolić L, Pevzner PA.

mspire 0.10.8 – Mass Spectrometry Proteomics in Ruby

mspire 0.10.8

:: DESCRIPTION

Mspire is a full featured library for working with mass spectrometry data, particularly proteomic, metabolomic and lipidomic data sets. It aims to be fast, robust, and beautiful.

::DEVELOPER

Prince Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Ruby

:: DOWNLOAD

 mspire

:: MORE INFORMATION

Citation

Prince JT, Marcotte EM.
mspire: mass spectrometry proteomics in Ruby.
Bioinformatics. 2008 Dec 1;24(23):2796-7.

peakANOVA – Stronger Findings from Mass Spectral data through Multi-peak Modeling

peakANOVA

:: DESCRIPTION

peakANOVA is a hierarchical Bayesian model for inferring differences between groups of samples more accurately in metabolomic studies, where the observed compounds are collinear.

::DEVELOPER

Probabilistic Machine Learning

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java/ R

:: DOWNLOAD

 peakANOVA

:: MORE INFORMATION

Citation

Stronger findings for metabolomics through Bayesian modeling of multiple peaks and compound correlations.
Suvitaival T, Rogers S, Kaski S.
Bioinformatics. 2014 Sep 1;30(17):i461-7. doi: 10.1093/bioinformatics/btu455

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.

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.

SRPI – Score Regularization for Peptide Identification

SRPI

:: DESCRIPTION

SRPI is a score regularization method which can be used as a general post-processing step for improving peptide identifications.

::DEVELOPER

Laboratory for Bioinformatics and Computational Biology, HKUST

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 SRPI

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S2. doi: 10.1186/1471-2105-12-S1-S2.
Score regularization for peptide identification.
He Z1, Zhao H, Yu W.

PeptideReranking – Peptide Re-ranking with Protein-peptide Correspondence and Precursor Peak Intensity Information

PeptideReranking

:: DESCRIPTION

PeptideReranking includes three peptide reranking methods: PPMRanker, PPIRanker, and MIRanker. PPMRanker only uses Protein-Peptide Map (PPM) information from the protein database, PPIRanker only uses Precursor Peak Intensity (PPI) information, and MIRanker employs both PPM information and PPI information.

::DEVELOPER

Laboratory for Bioinformatics and Computational Biology, HKUST

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PeptideReranking

:: MORE INFORMATION

Citation:

IEEE/ACM Trans Comput Biol Bioinform. 2012 Jul-Aug;9(4):1212-9. doi: 10.1109/TCBB.2012.29.
Peptide reranking with protein-peptide correspondence and precursor peak intensity information.
Yang C1, He Z, Yang C, Yu W.

MOTIPS – Motif Analysis Pipeline

MOTIPS

:: DESCRIPTION

MOTIPS employs an efficient search algorithm to scan a target proteome for potential domain targets and to increase the accuracy of each hit by integrating a variety of pre-computed features, such as conservation, surface propensity, and disorder.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Web Server
  • Java

:: DOWNLOAD

MOTIPS 

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2010 May 11;11:243. doi: 10.1186/1471-2105-11-243.
MOTIPS: automated motif analysis for predicting targets of modular protein domains.
Lam HY, Kim PM, Mok J, Tonikian R, Sidhu SS, Turk BE, Snyder M, Gerstein MB.

BatMass 0.3.1 – Mass Spectrometry data Visualization

BatMass 0.3.1

:: DESCRIPTION

BatMass is a mass-spectrometry data visualization tool, with the main focus on being fast and interactive while providing comprehensive visualizations without any parameter tweaking.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOs
  • Java

:: DOWNLOAD

BatMass

:: MORE INFORMATION

Citation:

J Proteome Res. 2016 Aug 5;15(8):2500-9. doi: 10.1021/acs.jproteome.6b00021. Epub 2016 Jun 28.
BatMass: a Java Software Platform for LC-MS Data Visualization in Proteomics and Metabolomics.
Avtonomov DM, Raskind A, Nesvizhskii AI.