Bioinformatics for LC-MS/MS-Based Proteomics - LC-MS/MS in Proteomics: Methods and Applications - page 69

Table 4.4
Visualization of LC-MS/MS data, validating, comparing, and
reporting results software

Visualization of LC-MS/MS data
MSight ( 94 ) http://www.expasy.ch/MSight /

Pep3D ( 95 ) http://tools.proteomecenter.org/wiki/index.php?

title = Software:Pep3D

DeCyder MS http://www5.gelifesciences.com/aptrix/upp01077.

nsf/Content/Products?OpenDocument&parentid
= 976024&moduleid = 166070&zone = Elpho

Prequips ( 96 ) http://prequips.sourceforge.net/
Validating and comparing search results
Scaffold ( 30 ) http://www.proteomesoftware.com /

PROTEOIQ https://www.bioinquire.com/

Proteome
Discoverer

http://www.thermo.com/com/cda/product/
detail/1,1055,10142329,00.html

Phenyx ( 81 ) http://www.genebio.com/products/phenyx /

Trans-Proteomic
Pipeline ( 77 )

http://tools.proteomecenter.org/wiki/index.php?
title = Software:TPP
IDPicker ( 97 ) http://fenchurch.mc.vanderbilt.edu/bumbershoot/
idpicker/index.html
DTASelect ( 98 ) http://fields.scripps.edu/DTASelect/
Reporting search results
Excel (Microsoft) http://office.microsoft.com/en-us/excel/default.

aspx

Mascot Parser http://www.matrixscience.com/msparser.html

MASCOT
HTML
and XML
parser ( 32 )

http://www.ccbm.jhu.edu

MascotDatfile
( 33 )

http://genesis.ugent.be/MascotDatfile/

mres2x ( 34 ) http://grosse-coosmann.de/ ∼ florian/Overview.

html

Scaffold ( 30 ) http://www.proteomesoftware.com /

PROTEOIQ https://www.bioinquire.com/

Multiplierz ( 99 ) http://blais.dfci.harvard.edu/multiplierz/

MassSieve ( 100 ) http://www.ncbi.nlm.nih.gov/staff/

slottad/MassSieve /

MASPECTRAS
( 101 )

https://maspectras.genome.tugraz.at/maspectras/

VEMS ( 17 ) http://personal.cicbiogune.es/rmatthiesen/

MascotDatfile
( 33 )

http://genesis.ugent.be/MascotDatfile/

(Continued)