apLCMS 6.6.6 – adaptive processing of high resolution LC/MS data

apLCMS 6.6.6

:: DESCRIPTION

apLCMS is an R package which designed for the processing of LC/MS based metabolomics data. It starts with a group of LC/MS files in the same folder, and generates a table with features in the rows and intensities in the columns.

::DEVELOPER

Tianwei Yu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

apLCMS

:: MORE INFORMATION

Citation

apLCMS–adaptive processing of high-resolution LC/MS data.
Yu T, Park Y, Johnson JM, Jones DP.
Bioinformatics. 2009 Aug 1;25(15):1930-6. doi: 10.1093/bioinformatics/btp291.

FT-ARM – Identification and Quantification of Multiplexed High-resolution

FT-ARM

:: DESCRIPTION

FT-ARM (Fourier transform-all reaction monitoring) is a software package which allows you to search and quantify peptides from data acquired in a multiplexed acquisition scheme. This data is typically acquired over some defined mass window during the entire chromatogram (ex. 700-800 m/z). Presently this software supports Thermo .raw files from any high resolution platform (ex. LTQ-FT, Orbitrap). However, we plan to extend support to all instrument vendors via the Proteowizard library.

::DEVELOPER

The Bruce Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 FT-ARM

:: MORE INFORMATION

Citation

Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification.
Weisbrod CR, Eng JK, Hoopmann MR, Baker T, Bruce JE.
J. Proteome Res., 2012, 11 (3), pp 1621–1632

savvy 0.1 – Generate High Resolution Print Quality Plasmid Map

savvy 0.1

:: DESCRIPTION

savvy is a CGI web app to generate high resolution print quality plasmid map using SVG.

::DEVELOPER

Malay K Basu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 savvy

:: MORE INFORMATION

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.

eQTNMiner 2.0.0 – High-resolution Mapping of Quantitative Trait Loci

eQTNMiner 2.0.0

:: DESCRIPTION

eQTNMiner (expression quantitative trait nucleotide Miner) is a computational package to carry out high-resolution mapping of quantitative trait loci (QTL) for high-dimensional genomic features like gene expression, epigenetic modifications, etc… and much more.

::DEVELOPER

Jean-Baptiste Veyrieras

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • GDL

:: DOWNLOAD

 eQTNMiner

:: MORE INFORMATION

Hardklör 1.36 – Analysis of High- resolution Mass Spectra

Hardklör 1.36

:: DESCRIPTION

Hardklör is a software application for the analysis of high- resolution mass spectra. It’s primary function is the deconvolution and determination of monoisotopic mass and charge state of single and overlapping protein/peptide isotope distributions contained in a mass spectra.

::DEVELOPER

MacCoss Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 Hardklör

:: MORE INFORMATION

Citation

Hoopmann MR, Finney GL, MacCoss MJ,
High speed data reduction, feature selection, and MS/MS spectrum quality assessment of shotgun proteomics datasets using high resolution mass spectrometry,
Anal. Chem., 79, 5630-5632 (2007)

ModRefiner 20111024 – High-resolution Protein Structure Refinement

ModRefiner 20111024

:: DESCRIPTION

ModRefiner is an algorithm for atomic-level, high-resolution protein structure refinement, which can start from either C-alpha trace, main-chain model or full-atomic model. Both side-chain and backbone atoms are completely flexible during structure refinement simulations, where conformational search is guided by a composite of physics- and knowledge-based force field. ModRefiner has an option to allow for the assignment of a second structure which will be used as a reference to which the refinement simulations are driven. One aim of ModRefiner is to draw the initial starting models closer to their native state, in terms of hydrogen bonds, backbone topology and side-chain positioning. It also generates significant improvement in physical quality of local structures. The standalone program also supports ab initio full-atomic relaxation, where the refined model is not restrainted by the initial model or the reference model.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows
:: DOWNLOAD

  ModRefiner for win, for linux

:: MORE INFORMATION

Citation

Dong Xu and Yang Zhang.
Improving Physical Realism and Structural Accuracy of Protein Models by a Two-step Atomic-level Energy Minimization
(in preparation).