MSAcquisitionSimulator 1.0.2 – Data-dependent Acquisition Simulator for LC-MS Shotgun Proteomics

MSAcquisitionSimulator 1.0.2

:: DESCRIPTION

MSAcquisitionSimulator is a collection of three command-line tools that simulate data-dependent acquisition algorithms on in silico generated ground truth data of liquid chromatography-mass spectrometry proteomics experiments.

::DEVELOPER

Major Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MSAcquisitionSimulator

:: MORE INFORMATION

Citation

MSAcquisitionSimulator: data-dependent acquisition simulator for LC-MS shotgun proteomics.
Goldfarb D, Wang W, Major MB.
Bioinformatics. 2015 Dec 17. pii: btv745.

SuperHirn 0.03 – High Resolution LC-MS-based Peptide/Protein Profiling

SuperHirn 0.03

:: DESCRIPTION

SuperHirn is a novel tool to quantitatively analyze multi dimensional LC-MS data in a label-free approach.

::DEVELOPER

Aebersold Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • C Compiler

:: DOWNLOAD

 SuperHirn

:: MORE INFORMATION

Citation

Proteomics. 2007 Oct;7(19):3470-80.
SuperHirn – a novel tool for high resolution LC-MS-based peptide/protein profiling.
Mueller LN1, Rinner O, Schmidt A, Letarte S, Bodenmiller B, Brusniak MY, Vitek O, Aebersold R, Müller M.

SILVER 1.1 – Stable Isotope Labeling LC-MS data Quantitative Analysis with Quality Control methods

SILVER 1.1

:: DESCRIPTION

SILVER is an efficient tool for quantification of the stable isotope labeling mass spectrometry data. SILVER implements novel methods for quality control of quantification at spectrum, peptide and protein levels respectively. Several new confidence filters and indices are applied to improve the accuracy of quantification results. Additionally, SILVER provides user-friendly interfaces for parameter setting, quantitative analysis, result visualization and manual validation as well as some useful statistics analyses.

::DEVELOPER

Bioinformatics Group, Beijing Proteome Research Center Bioinformatics Group

:: SCREENSHOTS

SILVER

:: REQUIREMENTS

  • Windows
  • Java

:: DOWNLOAD

 SILVER

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Feb 15;30(4):586-7. doi: 10.1093/bioinformatics/btt726. Epub 2013 Dec 15.
SILVER: an efficient tool for stable isotope labeling LC-MS data quantitative analysis with quality control methods.
Chang C1, Zhang J, Han M, Ma J, Zhang W, Wu S, Liu K, Xie H, He F, Zhu Y.

BPDA2d 1.0 – A 2D Global Optimization based Bayesian Peptide Detection algorithm for LC-MS

BPDA2d 1.0

:: DESCRIPTION

The BPDA2d software package can be used for peptide detection in LC-MS data with resolution high enough to baseline-resolve isotopic peaks. BPDA2d achieves peptide deisotoping and charge state deconvolution simultaneously. It systematically evaluates all possible combinations of possible peptide candidates for spectra interpretation, and optimizes peptide signals in order to minimize the mean squared error between inferred and observed spectra.

::DEVELOPER

BPDA2d team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 BPDA2d

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Feb 15;28(4):564-72. doi: 10.1093/bioinformatics/btr675. Epub 2011 Dec 6.
BPDA2d–a 2D global optimization-based Bayesian peptide detection algorithm for liquid chromatograph-mass spectrometry.
Sun Y1, Zhang J, Braga-Neto U, Dougherty ER.

MultiGlycan 1.0 – Annotation of Glycomic Profiles in the LC-MS data

MultiGlycan 1.0

:: DESCRIPTION

MultiGlycan helps user to gather glycan profile information from LC-MS Spectra. It also reports quantity of specific glycan composition.

::DEVELOPER

MultiGlycan team

:: SCREENSHOTS

MultiGlycan

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MultiGlycan

 :: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):1706-7. doi: 10.1093/bioinformatics/btt190. Epub 2013 Apr 22.
Automated annotation and quantification of glycans using liquid chromatography-mass spectrometry.
Yu CY1, Mayampurath A, Hu Y, Zhou S, Mechref Y, Tang H.

MetaboQC 1.0 – Evaluation of peak picking quality in LC-MS Metabolomics data

MetaboQC 1.0

:: DESCRIPTION

MetaboQC program is based on the analysis of discrepancies between replicate samples. It suggests the optimal parameters of peak-picking procedure and detects local discrepancies of the chromatogram alignment.

::DEVELOPER

Department of Plant Sciences,WIS

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MetaboQC

:: MORE INFORMATION

Citation

Brodsky, L., Moussaieff, A., Shahaf, N., Aharoni, A. and Rogachev, I. (2010)
Evaluation of peak picking quality in LC-MS Metabolomics data.
Analytical Chemistry, 82 :9177-9187.