Bioinformatics for LC-MS/MS-Based Proteomics - LC-MS/MS in Proteomics: Methods and Applications - page 75

Table 4.6
PTM and de novo sequencing software

PTM software
deltaMasses ( 111 ) http://www.detectorvision.com/deltaMasses.html

ModifiComb ( 57 ) http://www.medicwave.com/pas_modificomb.php

Spectral networks ( 55 ) http://bix.ucsd.edu/

Modiro http://www.modiro.com:8080/licenseserver/home.seam

POSTMan ( 59 ) http://www.probe.uib.no/software.php

Ascore ( 58 ) http://ascore.med.harvard.edu/

MS-Alignment ( 112 ) http://proteomics.ucsd.edu/

PhosCalc ( 113 ) http://www.ayeaye.tsl.ac.uk/PhosCalc /

SPIDER ( 88 ) http://www.bioinformaticssolutions.com/products/peaks/spider.php

Popitam ( 114 ) www.expasy.org/tools/popitam

De novo software
Mascot Distiller

http://www.matrixscience.com/distiller.html

Lutefisk ( 115 ) http://www.hairyfatguy.com/Lutefisk /

PEAKS ( 116 ) http://www.bioinformaticssolutions.com/products/peaks/db_

bsipaper.php

NovoHMM ( 117 ) http://people.inf.ethz.ch/befische/proteomics/

Audens ( 118 ) http://www.ti.inf.ethz.ch/pw/software/audens /

RAId ( 119 ) [e-mail]

SHERENGA ( 120 ) http://code.google.com/p/sherenga/

De novo search engines
PEAKS ( 116 ) http://www.bioinformaticssolutions.com/products/peaks/db_
bsipaper.php
PepNovo ( 121 ) http://proteomics.ucsd.edu/Software/PepNovo.html
Sequence-based search programs
MS-BLAST ( 122 ) dove.embl-heidelberg.de/Blast2/msblast.html
FASTS ( 123 ) http://fasta.bioch.virginia.edu/fasta_www2/fasta_www.cgi?rm = select&
pgm = fs
CIDentify ( 115 ) http://faculty.virginia.edu/wrpearson/fasta/OLD/CIDentify/
Multiple peptides from one spectra
ProbIDtree ( 124 )

http://sourceforge.net/project/showfiles.php?group_id = 69281&
package_id = 173843

Hardklör ( 125 ) http://proteome.gs.washington.edu/software/hardklor/

used to acquire the data and a fair amount of experience. It is
also a difficult computational task and there have been many dif-
ferent attempts at solving the de novo sequencing problem. The
majority of the programs use a spectrum graph and scoring system
approach but alternative methods using constraint satisfaction,