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.

SimTandem 1.1.96 – Protein Sequence Identification

SimTandem 1.1.96

:: DESCRIPTION

SimTandem is a freely available tool for identification of peptides from LC-MS/MS spectra. It is based on a similarity search of mass spectra in a database of theoretical spectra generated from a database of known protein sequences.

::DEVELOPER

SIRET Research Group

:: SCREENSHOTS

SimTandem

:: REQUIREMENTS

  • Windows/Linux
  • OpenMS

:: DOWNLOAD

 SimTandem

:: MORE INFORMATION

Citation:

Jiri Novak, Timo Sachsenberg, David Hoksza, Tomas Skopal and Oliver Kohlbacher.
On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications.
Journal of Integrative Bioinformatics, 10(3):228, 2013.

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

GOfact 20051017 – An Integrated Strategy for Functional Analysis in Large-scale Proteomic Research by Gene Ontology

GOfact 20051017

:: DESCRIPTION

GOfact is developed to identify the functional distribution and the significantly enriched functional categories of the proteomic expression profile. It would be helpful for understanding the overall functions of these identified proteins and supply the fundamental information for further bioinformatics exploration.

::DEVELOPER

The State Key Laboratory of Proteomics, Beijing Proteome Research Center (BPRC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows
  • Perl

:: DOWNLOAD

  GOfact

:: MORE INFORMATION

Citation

Li Dong, Li Jian-Qi, Ouyang Shu-Guang, Wang Jian, Xu Xiaojie, Zhu Yun-Ping, He Fu-Chu.
An Integrated Strategy for Functional Analysis in Large-scale Proteomic Research by Gene Ontology.
Biochemistry and Biophysics 2005,32(11):1026-1029

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.

TopPIC 1.2 – TOP-Down Mass Spectrometry Based Proteoform Identification and Characterization

TopPIC 1.2

:: DESCRIPTION

TopPIC is a software tool for identification and characterization of proteoforms at the whole proteome level by top-down tandem mass spectra using database search.

::DEVELOPER

Xiaowen Liu ,CCMS The Center for Computational Mass Spectrometry

:: REQUIREMENTS

  • Linux/windows

:: DOWNLOAD

 TopPIC

:: MORE INFORMATION

Citation:

TopPIC: A software tool for top-down mass spectrometry-based proteoform identification and characterization.
Kou Q, Xun L, Liu X.
Bioinformatics. 2016 Jul 16. pii: btw398.

Protein identification using top-down spectra.
Liu X, Sirotkin Y, Shen Y, Anderson G, Tsai YS, Ting YS, Goodlett DR, Smith RD, Bafna V, Pevzner PA.
Mol Cell Proteomics. 2012 Jun;11(6):M111.008524. doi: 10.1074/mcp.M111.008524.

PSS 20091105 – Protein Profile Similarity Screening

PSS 20091105

:: DESCRIPTION

PSS is a matlab code of computational protein profile similarity screening for quantitative mass spectrometry experiments.

::DEVELOPER

Hamprecht lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 PSS

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jan 1;26(1):77-83. doi: 10.1093/bioinformatics/btp607. Epub 2009 Oct 27.
Computational protein profile similarity screening for quantitative mass spectrometry experiments.
Kirchner M1, Renard BY, Köthe U, Pappin DJ, Hamprecht FA, Steen H, Steen JA.

Mass-Up 1.0.9 – Mass Spectrometry Utility for Proteomics

Mass-Up 1.0.9

:: DESCRIPTION

Mass-Up is an open-source mass spectrometry software for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data.

::DEVELOPER

The SING research group

:: SCREENSHOTS

Mass-Up

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • Java

:: DOWNLOAD

 Mass-Up

:: MORE INFORMATION

Citation:

Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery.
López-Fernández H, Santos HM, Capelo JL, Fdez-Riverola F, Glez-Peña D, Reboiro-Jato M.
BMC Bioinformatics. 2015 Oct 5;16(1):318. doi: 10.1186/s12859-015-0752-4.

MRMPlusGUI 20151104 – Quality Control and Assessment tool for SRM/MRM Assay development

MRMPlusGUI 20151104

:: DESCRIPTION

MRMPlusGUI is a freely available, open-source tool in the platform independent Java programming language to compute analytical measures as recommended recently by the Clinical Proteomics Tumor Analysis Consortium Assay Development Working Group for “Tier 2” assays.

::DEVELOPER

MRMPlusGUI team

:: SCREENSHOTS

MRMPlus

:: REQUIREMENTS

  • MacOsX/Linux / Windows
  • Java

:: DOWNLOAD

 MRMPlusGUI

:: MORE INFORMATION

Citation

MRMPlus: an open source quality control and assessment tool for SRM/MRM assay development.
Aiyetan P, Thomas SN, Zhang Z, Zhang H.
BMC Bioinformatics. 2015 Dec 12;16(1):411. doi: 10.1186/s12859-015-0838-z.