JAMSS – A GUI Java Mass Spectrometry Simulation Suite

JAMSS

:: DESCRIPTION

JAMSS is a fast, self-contained in silico simulator capable of generating simulated MS and LC- MS runs while providing meta information on the provenance of each generated signal.

::DEVELOPER

Rob Smith

:: SCREENSHOTS

JAMSS

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • Java

:: DOWNLOAD

 JAMSS

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Nov 3. pii: btu729.
JAMSS: Proteomics Mass Spectrometry Simulation in Java.
Smith R1, Prince JT

MAGIC V1.0.1 / MAGIC-web – Mass Spectrometry-based Automated Glycopeptide IdentifiCation platform

MAGIC V1.0.1 / MAGIC-web

:: DESCRIPTION

MAGIC is an automated tool for glycopeptide identification and glycan composition determination.

MAGIC-web is a web server aiming to provide mass spectrometry-based automated glycoprotein identification service.

::DEVELOPER

Computational Omic Labortary

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MAGIC

:: MORE INFORMATION

Citation

MAGIC-web: a platform for untargeted and targeted N-linked glycoprotein identification.
Lih TM, Choong WK, Chen CC, Cheng CW, Lin HN, Chen CT, Chang HY, Hsu WL, Sung TY.
Nucleic Acids Res. 2016 Apr 15. pii: gkw254

Anal Chem. 2015 Feb 17;87(4):2466-73. doi: 10.1021/ac5044829. Epub 2015 Jan 28.
MAGIC: an automated N-linked glycoprotein identification tool using a Y1-ion pattern matching algorithm and in silico MS2 approach.
Lynn KS1, Chen CC, Lih TM, Cheng CW, Su WC, Chang CH, Cheng CY, Hsu WL, Chen YJ, Sung TY.

BiMS 1.0 – Biclustering for Mass Spectrometry data

BiMS 1.0

:: DESCRIPTION

BiMS is a Java application designed to allow the application of biclustering algorithms to mass spectrometry datasets.

::DEVELOPER

SING Group.

:: SCREENSHOTS

BiMS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • JRE
  • R

:: DOWNLOAD

 BiMS

:: MORE INFORMATION

Citation

H. López-Fernández, M. Reboiro-Jato, Sara C. Madeira, Rubén López Cortés, J. D. Nunes-Miranda, H. M. Santos, Florentino Fdez-Riverola, Daniel Glez-Peña
A Workflow for the Application of Biclustering to Mass Spectrometry Data
7th International Conference on Practical Applications of Computational Biology & Bioinformatics – Advances in Intelligent Systems and Computing, 222, 2013, pp. 145-153. ISBN: 978-3-319-00577-5 (Print) 978-3-319-00578-2 (Online)

Mass-Up 1.0.9 – Mass Spectrometry Utility for Proteomics

Mass-Up 1.0.9

:: DESCRIPTION

Mass-Up is an open-source mass spectrometry software for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data.

::DEVELOPER

The SING research group

:: SCREENSHOTS

Mass-Up

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • Java

:: DOWNLOAD

 Mass-Up

:: MORE INFORMATION

Citation:

Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery.
López-Fernández H, Santos HM, Capelo JL, Fdez-Riverola F, Glez-Peña D, Reboiro-Jato M.
BMC Bioinformatics. 2015 Oct 5;16(1):318. doi: 10.1186/s12859-015-0752-4.

PhosSA – Phosphorylation Site Assignment Algorithm for Mass Spectrometry Data

PhosSA

:: DESCRIPTION

PhosSA is a program for phosphorylation site assignment of LC-MS/MS data. It uses a linear-time and linear space dynamic programming strategy for phosphorylation site assignment. The algorithm optimizes the objective function defined as the summation of intensity peaks that are associated with theoretical peptide fragmentation ions. A classifier introduced in the algorithm exploits the specific characteristics of mass spectrometry data to distinguish between the correctly and incorrectly assigned site(s).

::DEVELOPER

Epithelial Systems Biology Laboratory

:: SCREENSHOTS

PhosSA

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • JRE

:: DOWNLOAD

PhosSA

:: MORE INFORMATION

Citation

Proteome Sci. 2013 Nov 7;11(Suppl 1):S14. doi: 10.1186/1477-5956-11-S1-S14. Epub 2013 Nov 7.
PhosSA: Fast and accurate phosphorylation site assignment algorithm for mass spectrometry data.
Saeed F, Pisitkun T, Hoffert JD, Rashidian S, Wang G, Gucek M, Knepper MA.

Crux 2.1 – Tandem Mass Spectrometry Analysis

Crux 2.1

:: DESCRIPTION

Crux analyzes shotgun proteomics tandem mass spectra, associating peptides with observed spectra.

::DEVELOPER

Noble Research Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 Crux

:: MORE INFORMATION

Citation:

Crux: rapid open source protein tandem mass spectrometry analysis.
McIlwain S, Tamura K, Kertesz-Farkas A, Grant CE, Diament B, Frewen B, Howbert JJ, Hoopmann MR, Käll L, Eng JK, MacCoss MJ, Noble WS.
J Proteome Res. 2014 Oct 3;13(10):4488-91. doi: 10.1021/pr500741y.

SpectroGene 1.0 – Genome Annotation using Top-down Mass Spectrometry

SpectroGene 1.0

:: DESCRIPTION

SpectroGene is a tool for top-down protein identification using unannotated bacterial genome.

::DEVELOPER

SpectroGene team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 SpectroGene

:: MORE INFORMATION

Citation:

SpectroGene: a tool for proteogenomic annotations using top-down spectra.
Kolmogorov M, Liu X, Pevzner PA.
J Proteome Res. 2015 Dec 2.

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.

ProSight Lite 1.3 – Analyze Top-down Mass Spectrometry data

ProSight Lite 1.3

:: DESCRIPTION

ProSight Lite is a free Windows application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations.

::DEVELOPER

Proteomics Center of Excellence

:: SCREENSHOTS

ProSight

:: REQUIREMENTS

  • Windows
  • Visual C++ 2013 Runtime Libraries (x86)
  • Microsoft .NET Framework 4.5.1 (x86 and x64)

:: DOWNLOAD

 ProSight Lite

:: MORE INFORMATION

Citation

Proteomics. 2014 Dec 12. doi: 10.1002/pmic.201400313. [Epub ahead of print]
ProSight Lite: Graphical software to analyze top-down mass spectrometry data.
Fellers RT1, Greer JB, Early BP, Yu X, LeDuc RD, Kelleher NL, Thomas PM.

SIRIUS 3.0.3 – Identification of Metabolites using single and Tandem Mass Spectrometry

 Sirius 3.0.3

:: DESCRIPTION

Sirius ,(Sum formula Identification by Ranking Isotope patterns Using mass Spectrometry) a new java-based software framework for discovering a landscape of de-novo identification of metabolites using single and tandem mass spectrometry. Sirius2 deduces molecular formulas of small compounds by ranking isotope patterns from mass spectra of high resolution. Sirius2 further analyses the fragmentation pattern of a compound resulting in hypothetical fragmentation trees. It allows for automated and high-throughput analysis of small-compound MS data beyond elemental composition without requiring compound structures or a mass spectral database.

::DEVELOPER

Lehrstuhl Bioinformatik Jena

:: SCREENSHOTS

SIRIUS

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

   Sirius

:: MORE INFORMATION

Citation:

SIRIUS: decomposing isotope patterns for metabolite identification
Sebastian B?cker, Matthias C. Letzel, Zsuzsanna Lipták and Anton Pervukhin
Bioinformatics (2009) 25 (2): 218-224