PowerGet 3.5.7 – Software for liquid chromatography (LC) – high-resolution mass spectrometers (MS).

PowerGet 3.5.7

:: DESCRIPTION

PowerGet is a suite of data analytical tools developed for liquid chromatography (LC) – high-resolution mass spectrometers (MS).

::DEVELOPER

Kazusa DNA Research Institute

:: SCREENSHOTS

PowerGet

:: REQUIREMENTS

  • Windows
  • Java Runtime Environment

:: DOWNLOAD

 PowerGet

:: MORE INFORMATION

SimLipid 4.40 – Characterize lipids using Data from MS, MS/MS and MSE

SimLipid 4.40

:: DESCRIPTION

SimLipid is a comprehensive informatics tool for characterizing lipids using precursors and product ions data from MS, MS/MS and MSE data.

Lipidomics is an emerging field of systems biology being applied to disease research, drug discovery and biomarker identification. Mass spectrometry is one of the most sophisticated technologies for identification and quantification of lipids from biological mixtures. However, the major challenge in mass spectrometric data analysis is the huge amount of data generated in the process. Some of the most important aspects of mass spectrometric lipidome data analysis are the high throughput quantitative analysis of crude lipid extracts and structural identification of lipids using precursor and product ion data.

::DEVELOPER

PREMIER Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

SimLipid DemoGet a free Key

:: MORE INFORMATION

Order SimLipid

ms 20140908 – Generating Samples under Neutral Models of Genetic Variation

ms 20140908

:: DESCRIPTION

ms is a program to generate samples under a variety of neutral models. The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets.

::DEVELOPER

Richard R. Hudson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 ms

:: MORE INFORMATION

Citation:

Richard R. Hudson (2002).
Generating samples under a Wright-Fisher neutral model of genetic variation.
Bioinformatics 18: 337-338.

MaXIC-Q v1 – MS/MS- and MS-based Quantitation Analysis

MaXIC-Q v1

:: DESCRIPTION

MaXIC-Q is an automated quantitation tool, which utilizes XICs acquired from isotope labeling techniques for quantitation analysis.

::DEVELOPER

Computational Omic Labortary

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MaXIC-Q

:: MORE INFORMATION

Citation

Chih-Chiang Tsou, Yin-Hao Tsui, Yi-Hwa Yian, Yi-Ju Chen, Han-Yin Yang, Chuan-Yih Yu, Ke-Shiuan Lynn, Yu-Ju Chen, Ting-Yi Sung, and Wen-Lian Hsu,
MaXIC-Q Web: a fully automated web service using statistical and computational methods for protein quantitation based on stable isotope labeling and LCMS,”
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W661-9. doi: 10.1093/nar/gkp476.

msstats 0.3.4 / msff 0.1.6 – Calculates Statistcs of Data from Hudson’s Coalescent Simulation program MS

msstats 0.3.4 / msff 0.1.6

:: DESCRIPTION

msstats Reads in data from Hudson’s coalescent simulation program ms and calculates several common summary statistcs.

msff Applies a frequency filter to the output of Dick Hudson’s coalescent simulation.

::DEVELOPER

Thornton Lab at UC Irvine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 msstats / msff

:: MORE INFORMATION

msABC 20120315 – Modification of Hudson’s ms to facilitate Multi-locus ABC analysis

msABC 20120315

:: DESCRIPTION

msABC is a program for simulating various neutral evolutionary demographic scenarios based on the software ms (Hudson 2002). msABC extends ms, calculating a multitude of summary statistics. Therefore, msABC is suitable for performing the sampling step of an Approximate Bayesian Computation analysis (ABC), under various neutral demographic models.

::DEVELOPER

Pavlos Pavlidis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
  • R package

:: DOWNLOAD

 msABC

:: MORE INFORMATION

Citation:

Mol Ecol Resour. 2010 Jul;10(4):723-7. doi: 10.1111/j.1755-0998.2010.02832.x. Epub 2010 Feb 2.
msABC: a modification of Hudson’s ms to facilitate multi-locus ABC analysis.
Pavlidis P, Laurent S, Stephan W.

MFPaQ 4.0.0 – Parse, Validate, and Quantify MS Proteomics Data

MFPaQ 4.0.0

:: DESCRIPTION

MFPaQ (Mascot File Parsing and Quantification ) is a new web application dedicated to parse, validate, and quantify proteomics data. It allows fast and user-friendly verification of Mascot result files, as well as data quantification using isotopic labeling methods (SILAC/ICAT) or label free approaches (spectral counting, MS signal comparison).

::DEVELOPER

the MFPaQ developper

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsx
  • Firefox 2 or higher
  • Mascot server 2.1 or higher
  • Apache
  • Perl

:: DOWNLOAD

 MFPaQ

:: MORE INFORMATION

Citation

Bouyssié D, Gonzalez de Peredo A, Mouton E, Albigot R, Roussel L, Ortega N, Cayrol C, Burlet-Schiltz O, Girard J-P, and Monsarrat B.
MFPaQ, a new software to parse, validate, and quantify proteomic data generated by ICAT and SILAC mass spectrometric analyses: application to the proteomic study of membrane proteins from primary human endothelial cells
Molecular & Cellular Proteomics, 6, 1621-1637

msHOT 20080815 – modifying ms that allows Hotspots of Recombination and Gene Conversion

msHOT 20080815

:: DESCRIPTION

msHOT, modifying Hudson’s ms simulator, allows for implementation of multiple crossover hotspots and/or multiple gene conversion hotspots in the simulated genetic region.

::DEVELOPER

Garrett Hellenthal and Matthew Stephens

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 msHOT

:: MORE INFORMATION

Citation:

Hellenthal, G and M. Stephens.
msHOT: modifying Hudson’s ms simulator to incorporate crossover and gene conversion hotspots.
Bioinformatics. 2007 Feb 15;23(4):520-1.

IRMa 1.31.1 – Validation of MS Peptides Identification

IRMa 1.31.1

:: DESCRIPTION

IRMa ( Interprétation des Résultats Mascot)  toolbox provides an interactive application to assist in the validation of Mascot® search results. IRMa reads MASCOT® result (using Matrix Science® Parser distributed free of charge) and automatically filters identified peptides. All relevant information is displayed in a structured manner, showing “proteins hits” details. User can then manually or automatically confirm or reject individual peptide spectrum matches.

::DEVELOPER

Christophe Bruley

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsx
  • Java

:: DOWNLOAD

 IRMa

:: MORE INFORMATION

Citation

Veronique Dupierris; Christophe Masselon; Magali Court; Sylvie Kieffer-Jaquinod; Christophe Bruley
A toolbox for Validation of mass spectrometry peptides identification and Generation of database: IRMa
Bioinformatics 2009;25 (15): 1980-1981. doi: 10.1093/bioinformatics/btp301

PyNISTPL – Python module that Interfaces to the NIST MS Search Engine libraries

PyNISTPL

:: DESCRIPTION

PyNISTPL is a python module that interfaces to the NIST MS Search Engine libraries to provide easy to use command-line searching and construction of peptide spectrum libraries.

::DEVELOPER

Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 PyNISTPL

:: MORE INFORMATION