Wikiomics:Protein mass spectrometry: Difference between revisions
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= | Protein mass spectrometry can be divided into: | ||
* identification of proteins/peptides | |||
* quantification | |||
* [http:// | |||
=Protein/peptide identification= | |||
==Peptide Mass Fingerprinting (PMF) or (MS)== | |||
Old method, superseded by MS/MS | |||
* algorithms: | |||
** [http://www.matrixscience.com/home.html Mascot] (gives probabilistic score) | |||
** [http://www.expasy.org/tools/aldente/ Aldente] | |||
** [http://prowl.rockefeller.edu/prowl-cgi/profound.exe ProFound ProFound] | |||
* caveats | |||
** no sequence information | |||
** journals started to require that at least one peptide of a protein identified by PMF should be confirmed by MS/MS | |||
==Peptide fragment fingerprinting (PFF) or (MS/MS)== | |||
* algorithms (most commonly used): | |||
** [http://fields.scripps.edu/sequest/index.html Sequest] $$$ | |||
** [http://www.matrixscience.com/home.html Mascot] $$$ | |||
** [http://pubchem.ncbi.nlm.nih.gov/omssa/ OMSSA] Open Mass Spectrometry Search Algorithm, open source | |||
** [http://thegpm.org/ XTandem] open source effort from Canada | |||
* [http:// | * algorithms (other/new/experimental): | ||
** [http://www.chem.agilent.com/scripts/pds.asp?lpage=7771 Spectrum Mill] $$$ | |||
** [http://compbio.ornl.gov/MASPIC/distribution/ MASPIC ] | |||
*** this paper claims 5-15% more confident hits than Sequest: [http://pubs.acs.org/cgi-bin/article.cgi/ancham/2005/77/i23/html/ac0501745.html] | |||
** [http://peptide.ucsd.edu/Software/Inspect.html InsPecT] A new variable mods search from Pevzner & Tanner @UCSD (free?) | |||
= | * filtering of the results | ||
** Trans Proteomic Pipeline [http://tools.proteomecenter.org/TPP.php] (free?) | |||
*** download from [http://sourceforge.net/project/showfiles.php?group_id=69281 Sourceforge] (TPP Cygwin Setup for Windows or 'Trans-Proteomic Pipeline' for Linux) | |||
*** commercial offshot [http://www.insilicos.com/IPP.html IPP] | |||
*** wiki devoted to TPP [http://tools.proteomecenter.org/wiki/index.php?title=Main_Page TPP_Wiki] | |||
*** dynamic newsgroup: [http://groups.google.com/group/spctools-discuss spctools-discuss] | |||
** [http://fields.scripps.edu/DTASelect/index.html DTASelect] it seems to be in a semi-frozen state (free for nonprofit but requires signed MTA) | |||
== | ==Databases== | ||
Use (if possible): | |||
* [http://www.ebi.ac.uk/IPI/IPIhelp.html IPI] International Protein Index | |||
* always use target-decoy database (i.e. concatenated: human_IPI + reversed_human_IPI) | |||
* decoy databases creation methods: | |||
** protein reversal (simple) | |||
*** MEGGAYGAGKAGGAFDPYTL -=> LTYPDFAGGAKGAGYAGGEM | |||
** peptide pseudo-reversal (used in Sorcerer by Sage-N Research) | |||
*** MEGGAYGAGKAGGAFDPYTL => (trypsin digest, used [http://169.230.19.26:8080/prospector/4.27.1/cgi-bin/msform.cgi?form=msdigest Ms-Digest]) MEGGAYGAGK AGGAFDPYTL => GAGYAGGEMK-ALTYPDFAGG (each peptide reversed, but trypsin digestion site preserved -> guessed from the Elias 2007 paper) | |||
** shuffled | |||
*** MEGGAYGAGKAGGAFDPYTL => FYAGADEAGMGTYKGGAGLP (used [http://host9.bioinfo3.ifom-ieo-campus.it/sms2/shuffle_protein.html SMS], results differ each time) | |||
** random (i.e. creating database of random proteins based on frequency of AA in source fasta file) | |||
* to create decoy database use [http://genesis.ugent.be/dbtoolkit/ DBToolkit] free java standalone | |||
== | ==de novo sequence determination algorithms== | ||
* PepNovo: [http://darwin.informatics.indiana.edu/col/meeting/2005_10/PepNovo.pdf (PDF)] | |||
* Sherenga [http://www.liebertonline.com/doi/pdfplus/10.1089/106652799318300 (PDF)] | |||
* Peaks [http://www.bioinformatics.uwaterloo.ca/papers/03peaks.pdf (PDF)] | |||
* Lutefisk [http://www.hairyfatguy.com/Lutefisk/ web] | |||
== | ==Spectral matching == | ||
* [http://p3.thegpm.org/tandem/ppp.html P3 (server)] from Global Proteomics Machine (free) | |||
** [http://www.thegpm.org/PPP/index.html description] | |||
* [http://www.peptideatlas.org/spectrast/ SpectraST] from ISB, Seattle (not as many species/options as P3) | |||
* [http://proteome.gs.washington.edu/software/bibliospec/documentation/index.html BiblioSpec] from MacCoss lab. (free for non-profit, online licence) | |||
** command line only | |||
* | |||
=Web sites= | |||
* [http://peptide.ucsd.edu/Software.html UCSD (Pevzner)] | |||
* [http://proteome.gs.washington.edu/ U. of Washington (MacCoss)] | |||
* [http://www.proteomecommons.org/tools.jsp Proteome Commons] collection of tools & links | |||
* | =Reviews= | ||
For a good review of programs and aspects of protein identification by mass spectrometry | |||
see: | |||
* [http://www3.interscience.wiley.com/cgi-bin/fulltext/112139941/HTMLSTART Hernandez et al. 2006 (HTML)] | |||
* | * [http://www3.interscience.wiley.com/cgi-bin/fulltext/113344091/PDFSTART Palagi et al. 2006 (PDF)] | ||
* | * [http://www3.interscience.wiley.com/cgi-bin/fulltext/112098427/PDFSTART Shadforth et al. 2005 (PDF)] | ||
==Other tools to be sorted out== | |||
* massSorter [http://www.bioinfo.no/software/massSorter] | |||
* ProteinProspector [http://prospector.ucsf.edu/] | |||
* Sonar [http://bioinformatics.genomicsolutions.com/service/prowl/sonar.html] | * Sonar [http://bioinformatics.genomicsolutions.com/service/prowl/sonar.html] | ||
* DeNovoID [http://proteomics.mcw.edu/denovoid web] | * DeNovoID [http://proteomics.mcw.edu/denovoid web] | ||
* SPIDER [http://ieeexplore.ieee.org/iel5/9262/29416/01332434.pdf?tp=&isnumber=&arnumber=1332434 (PDF)] de novo + homology search in other species | * SPIDER [http://ieeexplore.ieee.org/iel5/9262/29416/01332434.pdf?tp=&isnumber=&arnumber=1332434 (PDF)] de novo + homology search in other species | ||
* OpenSea [http://pubs.acs.org/cgi-bin/article.cgi/jprobs/2005/4/i02/html/pr049781j.html (HTML)] Java program available from authors | * OpenSea [http://pubs.acs.org/cgi-bin/article.cgi/jprobs/2005/4/i02/html/pr049781j.html (HTML)] Java program available from authors | ||
* MSQuant [http://msquant.sourceforge.net/ MSQuant] Parser for Mascot results for quantitation. | * MSQuant [http://msquant.sourceforge.net/ MSQuant] Parser for Mascot results for quantitation. | ||
* ModifiComb [http://www.mcponline.org/cgi/content/full/5/5/935 (HTML)] (available from authors?) | * ModifiComb [http://www.mcponline.org/cgi/content/full/5/5/935 (HTML)] (available from authors?) | ||
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VEMS 3.0 | VEMS 3.0 | ||
MassSorter Eidhammer | MassSorter Eidhammer | ||
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Revision as of 11:40, 23 November 2007
Protein mass spectrometry can be divided into:
- identification of proteins/peptides
- quantification
Protein/peptide identification
Peptide Mass Fingerprinting (PMF) or (MS)
Old method, superseded by MS/MS
- algorithms:
- Mascot (gives probabilistic score)
- Aldente
- ProFound ProFound
- caveats
- no sequence information
- journals started to require that at least one peptide of a protein identified by PMF should be confirmed by MS/MS
Peptide fragment fingerprinting (PFF) or (MS/MS)
- algorithms (most commonly used):
- algorithms (other/new/experimental):
- Spectrum Mill $$$
- MASPIC
- this paper claims 5-15% more confident hits than Sequest: [1]
- InsPecT A new variable mods search from Pevzner & Tanner @UCSD (free?)
- filtering of the results
- Trans Proteomic Pipeline [2] (free?)
- download from Sourceforge (TPP Cygwin Setup for Windows or 'Trans-Proteomic Pipeline' for Linux)
- commercial offshot IPP
- wiki devoted to TPP TPP_Wiki
- dynamic newsgroup: spctools-discuss
- Trans Proteomic Pipeline [2] (free?)
- DTASelect it seems to be in a semi-frozen state (free for nonprofit but requires signed MTA)
Databases
Use (if possible):
- IPI International Protein Index
- always use target-decoy database (i.e. concatenated: human_IPI + reversed_human_IPI)
- decoy databases creation methods:
- protein reversal (simple)
- MEGGAYGAGKAGGAFDPYTL -=> LTYPDFAGGAKGAGYAGGEM
- peptide pseudo-reversal (used in Sorcerer by Sage-N Research)
- MEGGAYGAGKAGGAFDPYTL => (trypsin digest, used Ms-Digest) MEGGAYGAGK AGGAFDPYTL => GAGYAGGEMK-ALTYPDFAGG (each peptide reversed, but trypsin digestion site preserved -> guessed from the Elias 2007 paper)
- shuffled
- MEGGAYGAGKAGGAFDPYTL => FYAGADEAGMGTYKGGAGLP (used SMS, results differ each time)
- random (i.e. creating database of random proteins based on frequency of AA in source fasta file)
- protein reversal (simple)
- to create decoy database use DBToolkit free java standalone
de novo sequence determination algorithms
Spectral matching
- P3 (server) from Global Proteomics Machine (free)
- SpectraST from ISB, Seattle (not as many species/options as P3)
- BiblioSpec from MacCoss lab. (free for non-profit, online licence)
- command line only
Web sites
- UCSD (Pevzner)
- U. of Washington (MacCoss)
- Proteome Commons collection of tools & links
Reviews
For a good review of programs and aspects of protein identification by mass spectrometry see:
Other tools to be sorted out
- DeNovoID web
- SPIDER (PDF) de novo + homology search in other species
- OpenSea (HTML) Java program available from authors
- MSQuant MSQuant Parser for Mascot results for quantitation.
- ModifiComb (HTML) (available from authors?)
- MODi [6] web server for PTMs discovery
- UNIMOD [7] database of PTMs
- SILVER view your spectra with LOD scores