:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Prince JT, Marcotte EM.
mspire: mass spectrometry proteomics in Ruby.
Bioinformatics. 2008 Dec 1;24(23):2796-7.
:: DESCRIPTION
PAnalyzer is a software tool focused on the protein inference process of shotgun proteomics.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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)
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
The ms_lims project provides a lightweight, portable yet production-grade solution for managing mass spectrometry based proteomics data.
::DEVELOPER
Computational Omics and Systems Biology Group
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Proteomics. 2010 Mar;10(6):1261-4.
ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics.
Helsens K, Colaert N, Barsnes H, Muth T, Flikka K, Staes A, Timmerman E, Wortelkamp S, Sickmann A, Vandekerckhove J, Gevaert K, Martens L.
:: DESCRIPTION
InSilicoSpectro is a proteomics open-source project,aimed at implementing recurrent computations that are necessary for proteomics data analysis.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Proteome Res. 2006 Mar;5(3):619-24.
InSilicoSpectro: an open-source proteomics library.
Colinge J, Masselot A, Carbonell P, Appel RD.
:: DESCRIPTION
PWIMS is an information management system designed as client-server tool for handling Proteomics Experiments. It has features for 2DGe image capturing, Protocol Management, Mass spec data integration, sample management etc.
::DEVELOPER
Bioinformatics Group, Roskamp Institute
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Venkatarajan Mathura, Deepak Kolippakkam, Sarah Wilson, Freya Geall, Hong Wang, Fiona Crawford, Michael Mullan., 2004
“PWIMS 1.0: Proteomics Workflow and Information Management System”,
Society of Neuroscience, 34th Annual Meeting.
:: DESCRIPTION
PepDistiller is a software designed to validate the peptide identifications obtained from MASCOT search results.
::DEVELOPER
Beijing Proteome Research Center Bioinformatics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Proteomics. 2012 Jun;12(11):1720-5. doi: 10.1002/pmic.201100167.
PepDistiller: A quality control tool to improve the sensitivity and accuracy of peptide identifications in shotgun proteomics.
Li N, Wu S, Zhang C, Chang C, Zhang J, Ma J, Li L, Qian X, Xu P, Zhu Y, He F.
