Mass++ v2.7.4 – Analysis Tool for Mass Spectrometry

Mass++ v2.7.4

:: DESCRIPTION

Mass++ is freeware for mass spectrometry data analysis developed and released by our FIRST ms3d project. It can load data files of various mass spectrometers, display data with various kinds of views, and analyze data by various kinds of analysis functions.

::DEVELOPER

Koichi Tanaka Laboratory of Advanced Science and Technology

:: SCREENSHOTS

Mass

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Mass++

:: MORE INFORMATION

Citation:

J Proteome Res. 2014 Jul 7.
Mass++: A Visualization and Analysis Tool for Mass Spectrometry.
Tanaka S1, Fujita Y, Parry HE, Yoshizawa AC, Morimoto K, Murase M, Yamada Y, Yao J, Utsunomiya SI, Kajihara S, Fukuda M, Ikawa M, Tabata T, Takahashi K, Aoshima K, Nihei Y, Nishioka T, Oda Y, Tanaka K.

ProteinDecision 1.0 – Protein Identification using Peptide-Mass Fingerprinting Data

ProteinDecision 1.0

:: DESCRIPTION

ProteinDecision is a computer software for identifying protein by serching against protein database with the input Peptide-Mass Fingerprinting Data. It can handle the issues of selecting peaks from mass spectrum, transforming database format, displaying the top ranks of identification result, and detailed information for each ranking.

::DEVELOPER

Digital Biology Laboratory, University Of Missouri-Columbia

:: SCREENSHOTS

ProteinDecision

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 ProteinDecision

:: MORE INFORMATION

Citation

Methods Mol Biol. 2010;604:7-22. doi: 10.1007/978-1-60761-444-9_2.
Bioinformatics methods for protein identification using Peptide mass fingerprinting.
Song Z1, Chen L, Xu D.

metabosearch – Mass-based Metabolite Identification using multiple databases

metabosearch

:: DESCRIPTION

MetaboSearch performs mass-based metabolite search simultaneously against the four major metabolite databases: Human Metabolome DataBase (HMDB), Madison Metabolomics Consortium Database (MMCD), Metlin, and LipidMaps.

::DEVELOPER

Ressom Lab 

:: SCREENSHOTS

metabosearch

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 metabosearch

:: MORE INFORMATION

Citation

PLoS One. 2012;7(6):e40096. doi: 10.1371/journal.pone.0040096. Epub 2012 Jun 29.
MetaboSearch: tool for mass-based metabolite identification using multiple databases.
Zhou B1, Wang J, Ressom HW.

JMassBalance 20130207 – Mass-balanced Randomization and Analysis of Metabolic Networks

JMassBalance 20130207

:: DESCRIPTION

JMassBalance is a tool for mass-balanced randomization and analysis of metabolic networks. The tool allows efficient generation of large sets of randomized networks under the physical constraint of mass balance. In addition, various structural properties of the original and randomized networks can be calculated, facilitating the identification of the salient properties of metabolic networks with a biologically meaningful null model.

::DEVELOPER

Mathematical Modeling and Systems Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 JMassBalance

:: MORE INFORMATION

Citation

Georg Basler and Zoran Nikoloski (2011):
JMassBalance: mass-balanced randomization and analysis of metabolic networks.
Bioinformatics, 27(19):2761-2762. doi:10.1093/bioinformatics/btr448

MASS 5.0 – Meta-Analysis of Score Statistics

MASS 5.0

:: DESCRIPTION

The software MASS performs meta-analysis by combining the score statistics from K independent studies.The two approaches are asymptotically equivalent; however, the latter approach is numerically more stable and statistically more accurate, especially for discrete outcomes and unbalanced data (e.g., rare variants in case-control studies) (Lin and Tang, 2011). Another unique feature of MASS is its ability to perform multivariate meta-analysis.

::DEVELOPER

Danyu Lin

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 MASS

:: MORE INFORMATION

Citation

Lin DY, Tang ZZ. (2011).
A general framework for detecting disease associations with rare variants in sequencing studies.
The American Journal of Human Genetics, 89:354-367.

MassChroQ 2.0.1 – Mass Chromatogram Quantification

MassChroQ 2.0.1

:: DESCRIPTION

MassChroQ is a fast and versatile software that performs alignment, XIC extraction, peak detection and quantification on data obtained from Liquid Chromatography-Mass Spectrometry (LC-MS) techniques.

::DEVELOPER

pappso (Plate-forme d’analyses protéomiques de Paris Sud-Ouest)

:: SCREENSHOTS

MassChroQ

:: REQUIREMENTS

  • Windows/ MacOsX / Linux
  • Java

:: DOWNLOAD

 MassChroQ

:: MORE INFORMATION

Citation

Valot B, Langella O, Nano E, Zivy M, (2011),
MassChroQ: A versatile tool for mass spectrometry quantification,
Proteomics, 11:3572-3577.

MASS 1.0 – Multiple Protein Structure Alignment by Secondary Structures

MASS 1.0

:: DESCRIPTION

MASS is an efficient method for multiple alignment of protein structures and detection of structural motifs. Exploiting the secondary structure representation aids in filtering out noisy results and in making the method highly efficient and robust. MASS disregards the sequence order of the secondary structure elements. Thus, it can find non-sequential and even non-topological structural motifs. An important novel feature of MASS is subset alignment detection: It does not require that all the input molecules be aligned. Rather, MASS is capable of detecting structural motifs shared only by a subset of the molecules.

::DEVELOPER

 the BioInfo3D group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MASS

:: MORE INFORMATION

Citation:

O. Dror, H. Benyamini, R. Nussinov, and H. Wolfson .
MASS: Multiple structural alignment by secondary structures.
Bioinformatics, 19 Suppl. 1: i95 i104, 2003.