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.

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.

ProHits v4.0.3 – LIMS for Interaction Proteomics.

ProHits v4.0.3

:: DESCRIPTION

ProHits is an open source software package designed to help scientists store, search and analyze mass spectrometry data, in particular for protein-protein interaction experiments.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

ProHits

:: REQUIREMENTS

  • Linux
  • PHP
  • Apache
  • MYSQL.

:: DOWNLOAD

 ProHits

:: MORE INFORMATION

Citation:

F. Liu et al., (2010)
ProHits: an integrated software platform for mass spectrometry-based interaction proteomics.
Nat Biotech, 28:1015-7

Philosopher 2.0.0 – Toolkit for Shotgun Proteomics data analysis

Philosopher 2.0.0

:: DESCRIPTION

Philosopher provides easy access to third-party tools and custom algorithms for proteomics analysis, from database searching to functional protein reports. Philosopher is also well-equipped for open search analysis, providing extended versions of PeptideProphet and ProteinProphet for peptide validation and protein inference.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Philosopher

:: MORE INFORMATION

MSFragger / FragPipe 12.1 – Peptide Identification in Mass Spectrometry-based Proteomics

MSFragger / FragPipe 12.1

:: DESCRIPTION

MSFragger is an ultrafast database search tool that uses a fragment ion indexing method to rapidly perform spectra similarity comparisons.

FragPipe is a Java Graphical User Interface (GUI) for a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data. It is powered by MSFragger – an ultrafast proteomic search engine suitable for both conventional and “open” (wide precursor mass tolerance) peptide identification.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

MSFragger / FragPipe

:: MORE INFORMATION

Citation:

Andy Kong, Felipe Leprevost, Dmitry Avtonomov, Dattatreya Mellacheruvu, Alexey Nesvizhskii.
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics
Nat Meth, May 2017. DOI: 10.1038/nmeth.4256

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

DIA-Umpire 2.1.6 – Computational Analysis pipeline for DIA Proteomics data

DIA-Umpire 2.1.6

:: DESCRIPTION

DIA-Umpire is an open source Java program for computational analysis of data independent acquisition (DIA) mass spectrometry-based proteomics data. It enables untargeted peptide and protein identification and quantitation using DIA data, and also incorporates targeted extraction to reduce the number of cases of missing quantitation.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 DIA-Umpire

:: MORE INFORMATION

Citation:

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics.
Tsou CC, Avtonomov D, Larsen B, Tucholska M, Choi H, Gingras AC, Nesvizhskii AI.
Nat Methods. 2015 Mar;12(3):258-64, 7 p following 264. doi: 10.1038/nmeth.3255.

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)

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.