Category: proteomics

MSblender – Integrating Peptide Identifications from multiple database search engines

MSblender

:: DESCRIPTION

MSblender is a software for integrating peptide identifications from multiple database search engines. MSblender rescores unique peptide-spectrum matches by multivariate mixture modeling of score distributions from multiple search engines.

::DEVELOPER

the Marcotte Lab at University of Texas at Austin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C Compiler

:: DOWNLOAD

 MSblender 

:: MORE INFORMATION

Citation:

T. Kwon, H. Choi, C. Vogel, A.I. Nesvizhskii, and E.M. Marcotte,
MSblender: a probabilistic approach for integrating peptide identifications from multiple database search engines.
J. Proteome Res., 2011, 10 (7), pp 2949–2958

MAPDIA 3.1.0 – Model-based Analysis of quantitative Proteomics data in DIA-MS

MAPDIA 3.1.0

:: DESCRIPTION

mapDIA performs essential data preprocessing, including novel retention time-based normalization method and a sequence of peptide/fragment selection steps, and more importantly, hierarchical model-based statistical significance analysis for multi-group comparisons under representative experimental designs.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

 MAPDIA

:: MORE INFORMATION

Citation

mapDIA: Preprocessing and Statistical Analysis of Quantitative Proteomics Data from Data Independent Acquisition Mass Spectrometry.
Teo G, Kim S, Tsou CC, Collins B, Gingras AC, Nesvizhskii AI, Choi H.
J Proteomics. 2015 Sep 14. pii: S1874-3919(15)30130-5. doi: 10.1016/j.jprot.2015.09.013

Luciphor2 – PTM-site localization on MS/MS data

Luciphor2

:: DESCRIPTION

Luciphor2 is a site localization tool for generic post-translational modifications (PTMs) using tandem mass spectrometry data.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 Luciphor2

:: MORE INFORMATION

Citation:

Bioinformatics. 2015 Apr 1;31(7):1141-3. doi: 10.1093/bioinformatics/btu788. Epub 2014 Nov 25.
LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data.
Fermin D, Avtonomov D, Choi H, Nesvizhskii AI

QPROT 1.3.5 – Differential Protein Expression using Spectral Count and Intensity data.

QPROT 1.3.5

:: DESCRIPTION

QPROT is a software for differential protein expression using spectral count and intensity data. It also accounts for independent samples and paired samples.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 QPROT

:: MORE INFORMATION

Citation:

QPROT: Statistical method for testing differential expression using protein-level intensity data in label-free quantitative proteomics.
Choi H, Kim S, Fermin D, Tsou CC, Nesvizhskii AI.
J Proteomics. 2015 Nov 3;129:121-6. doi: 10.1016/j.jprot.2015.07.036.

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.

APEX 1.1.0 – Quantitative Proteomics Tool

APEX 1.1.0

:: DESCRIPTION

APEX (Absolute protein expression) Quantitative Proteomics Tool, is a free and open source Java implementation of the APEX technique for the quantitation of proteins based on standard LC- MS/MS proteomics data (Lu et al., Nature Biotech., 25(1):117-124, 2007). The underlying technique improves upon label free quantitation techniques such as MS/MS spectral counting. This technique uses machine learning algorithms to help correct for variable peptide detection related to certain peptide physicochemical properties which favor or hinder detection. The APEX tool provides a graphical user interface, an extensive integrated user help system, and a complete user’s manual. A sample data set and descriptive tutorial help to acquaint users with the operation of the tool. The APEX tool provides full support for all aspects of the APEX protein quantitation method and offers several utilities to help support downstream analysis. Please refer to the manual for a full description of the tool’s capabilities.

::DEVELOPER

the Marcotte Lab at University of Texas at Austin

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • JAVA

:: DOWNLOAD

APEX

:: MORE INFORMATION

Citation:

Peng Lu etc.
Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation,
Nature Biotechnology 25, 117 – 124 (2007)

PhosphoSiteAnalyzer 1.4 – Bioinformatical tool for Analyzing (Quantitative) Phosphoproteome datasets

PhosphoSiteAnalyzer 1.4

:: DESCRIPTION

PhosphoSiteAnalyzer is a novel bioinformatical tool for analyzing (quantitative) phosphoproteome datasets. The program retrieves kinase-substrate predictions from NetworKIN (Linding et al) and contains various statistical modules for futher analysis.

::DEVELOPER

PhosphoSiteAnalyzer team

:: SCREENSHOTS

PhosphoSiteAnalyzer

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  PhosphoSiteAnalyzer

:: MORE INFORMATION

Citation

PhosphoSiteAnalyzer: a bioinformatic platform for deciphering phospho proteomes using kinase predictions retrieved from NetworKIN.
Bennetzen MV, Cox J, Mann M, Andersen JS.
J Proteome Res. 2012 Jun 1;11(6):3480-6. doi: 10.1021/pr300016e.

ScreenCap3 – Screening of Caspase-3 substrates and Cleavage site prediction

ScreenCap3

:: DESCRIPTION

ScreenCap3 is a web-based prediction method, to facilitate the discovery of novel caspase-3 substrates in human proteome.

::DEVELOPER

Computational Biology Research Center[CBRC]

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Proteomics. 2014 Sep;14(17-18):2042-6. doi: 10.1002/pmic.201400002. Epub 2014 Aug 4.
ScreenCap3: Improving prediction of caspase-3 cleavage sites using experimentally verified noncleavage sites.
Fu SC, Imai K, Sawasaki T, Tomii K.

JAMSS – A GUI Java Mass Spectrometry Simulation Suite

JAMSS

:: DESCRIPTION

JAMSS is a fast, self-contained in silico simulator capable of generating simulated MS and LC- MS runs while providing meta information on the provenance of each generated signal.

::DEVELOPER

Rob Smith

:: SCREENSHOTS

JAMSS

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • Java

:: DOWNLOAD

 JAMSS

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Nov 3. pii: btu729.
JAMSS: Proteomics Mass Spectrometry Simulation in Java.
Smith R1, Prince JT

TPP 5.2 – Collection of integrated tools for MS/MS Proteomics

TPP 5.2

:: DESCRIPTION

TPP (Trans-Proteomic Pipeline) is a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to our open mzXML format.

::DEVELOPER

Seattle Proteome Center

:: SCREENSHOTS

TPP

:: REQUIREMENTS

  • Windows / Mac OsX / Linux

:: DOWNLOAD

  TPP 

:: MORE INFORMATION

Citation

Methods Mol Biol. 2010;604:213-38. doi: 10.1007/978-1-60761-444-9_15.
Trans-proteomic pipeline: a pipeline for proteomic analysis.
Pedrioli PG.