Tag: Mass Spectrometry

Crux 4.0 – Tandem Mass Spectrometry Analysis

Crux 4.0

:: 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.

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.

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 1.0.14 – Mass Spectrometry Utility for Proteomics

Mass-Up 1.0.14

:: 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.

MAGIC V1.0.2 / MAGIC-web – Mass Spectrometry-based Automated Glycopeptide IdentifiCation platform

MAGIC V1.0.2 / 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.

CRAPome v.0 – Contaminant Repository for Affinity Purification – Mass Spectrometry data

CRAPome 2.0

:: DESCRIPTION

CRAPome is a database of annotated negative controls contributed by the proteomics research community. It addresses the common problem of distinguishing real interactions from the non-specific background (also known as ‘contaminants’). The database and associated computational tools to score protein interactions are available online.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Nat Methods. 2013 Aug;10(8):730-6. doi: 10.1038/nmeth.2557. Epub 2013 Jul 7.
The CRAPome: a contaminant repository for affinity purification-mass spectrometry data.
Mellacheruvu D et al.

TBnovo – De novo Protein Sequencing by combining Top-down and Bottom-up Mass Spectrometry

TBnovo

:: DESCRIPTION

TBNovo is a de novo protein sequencing software tool which combines both top down and bottom up tandem mass spectra.

::DEVELOPER

Xiaowen Liu ,CCMS The Center for Computational Mass Spectrometry

:: REQUIREMENTS

  • Linux/Windows
  • JRE

:: DOWNLOAD

 TBnovo

:: MORE INFORMATION

Citation

J Proteome Res. 2014 Jul 3;13(7):3241-8. doi: 10.1021/pr401300m. Epub 2014 Jun 18.
De novo protein sequencing by combining top-down and bottom-up tandem mass spectra.
Liu X1, Dekker LJ, Wu S, Vanduijn MM, Luider TM, Tolić N, Kou Q, Dvorkin M, Alexandrova S, Vyatkina K, Paša-Tolić L, Pevzner PA.

mspire 0.10.8 – Mass Spectrometry Proteomics in Ruby

mspire 0.10.8

:: DESCRIPTION

Mspire is a full featured library for working with mass spectrometry data, particularly proteomic, metabolomic and lipidomic data sets. It aims to be fast, robust, and beautiful.

::DEVELOPER

Prince Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Ruby

:: DOWNLOAD

 mspire

:: MORE INFORMATION

Citation

Prince JT, Marcotte EM.
mspire: mass spectrometry proteomics in Ruby.
Bioinformatics. 2008 Dec 1;24(23):2796-7.

MARMoSET – Extracting Publication-ready Mass Spectrometry Metadata from RAW Files

MARMoSET

:: DESCRIPTION

MARMoSET (MetAdata fRom Mass SpectromETry) tool is intended to automatically extracts and reduces publication relevant metadata from Thermo Fischer Scientific RAW files.

::DEVELOPER

the Loosolab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R / C

:: DOWNLOAD

MARMoSET

:: MORE INFORMATION

Citation:

Kiweler M, Looso M and Graumann J.
MARMoSET – Extracting Publication-Ready Mass Spectrometry Metadata from RAW Files.
Mol Cell Proteomics, 18 (8), 1700-1702 (2019),

BatMass 0.3.1 – Mass Spectrometry data Visualization

BatMass 0.3.1

:: DESCRIPTION

BatMass is a mass-spectrometry data visualization tool, with the main focus on being fast and interactive while providing comprehensive visualizations without any parameter tweaking.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOs
  • Java

:: DOWNLOAD

BatMass

:: MORE INFORMATION

Citation:

J Proteome Res. 2016 Aug 5;15(8):2500-9. doi: 10.1021/acs.jproteome.6b00021. Epub 2016 Jun 28.
BatMass: a Java Software Platform for LC-MS Data Visualization in Proteomics and Metabolomics.
Avtonomov DM, Raskind A, Nesvizhskii AI.