Harvest: an open-source tool for the validation and improvement of peptide identification metrics and fragmentation exploration.
BACKGROUND
Protein identification using mass spectrometry is an important tool in many areas of the life sciences, and in proteomics research in particular. Increasing the number of proteins correctly identified is dependent on the ability to include new knowledge about the mass spectrometry fragmentation process, into computational algorithms designed to separate true matches of peptides to unidentified mass spectra from spurious matches. This discrimination is achieved by computing a function of the various features of the potential match between the observed and theoretical spectra to give a numerical approximation of their similarity. It is these underlying "metrics" that determine the ability of a protein identification package to maximise correct identifications while limiting false discovery rates. There is currently no software available specifically for the simple implementation and analysis of arbitrary novel metrics for peptide matching and for the exploration of fragmentation patterns for a given dataset.


RESULTS
We present Harvest: an open source software tool for analysing fragmentation patterns and assessing the power of a new piece of information about the MS/MS fragmentation process to more clearly differentiate between correct and random peptide assignments. We demonstrate this functionality using data metrics derived from the properties of individual datasets in a peptide identification context. Using Harvest, we demonstrate how the development of such metrics may improve correct peptide assignment confidence in the context of a high-throughput proteomics experiment and characterise properties of peptide fragmentation.


CONCLUSIONS
Harvest provides a simple framework in C++ for analysing and prototyping metrics for peptide matching, the core of the protein identification problem. It is not a protein identification package and answers a different research question to packages such as Sequest, Mascot, X!Tandem, and other protein identification packages. It does not aim to maximise the number of assigned peptides from a set of unknown spectra, but instead provides a method by which researchers can explore fragmentation properties and assess the power of novel metrics for peptide matching in the context of a given experiment. Metrics developed using Harvest may then become candidates for later integration into protein identification packages.
McHugh
Leo C
LC
Discipline of Medicine, Sydney Medical School, University of Sydney, Sydney, Australia.
Arthur
Jonathan W
JW
D000465:Algorithms; D001330:Electronic Data Processing; D010446:Peptide Fragments; D010455:Peptides / Q000032:analysis* / Q000737:chemistry; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*
D010446:Peptide Fragments; D010455:Peptides
Proteomics. 2003 Aug;3(8):1454-63
12923771
Anal Chem. 2002 Oct 15;74(20):5383-92
12403597
BMC Bioinformatics. 2007 Feb 09;8:51
17291342
Bioinformatics. 2008 Jul 1;24(13):i348-56
18586734
Pac Symp Biocomput. 2006;:219-30
17094241
PLoS Comput Biol. 2008 Feb;4(2):e12
18463710
Anal Chem. 2004 Jul 1;76(13):3556-68
15228325
J Chromatogr A. 2005 Jun 3;1077(1):1-18
15988981
J Proteome Res. 2004 Sep-Oct;3(5):958-64
15473683
J Proteome Res. 2003 Jan-Feb;2(1):43-50
12643542
Anal Chem. 2003 Nov 15;75(22):6251-64
14616009
Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18132-8
18818311
PLoS One. 2009 Dec 18;4(12):e8371
20020041
Electrophoresis. 1999 Dec;20(18):3551-67
10612281
J Am Soc Mass Spectrom. 1994 Nov;5(11):976-89
24226387
Bioinformatics. 2004 Dec 12;20(18):3628-35
15297302
Nature. 2003 Mar 13;422(6928):198-207
12634793
J Am Soc Mass Spectrom. 2007 May;18(5):850-5
17329120
J Mass Spectrom. 2000 Dec;35(12):1399-406
11180630
Bioinformatics. 2004 Aug 4;20 Suppl 1:i49-54
15262780
Anal Chem. 2000 Jun 1;72(11):2482-9
10857624
Proteomics. 2004 Mar;4(3):619-28
14997485
Proteomics. 2002 Oct;2(10):1406-12
12422357
Science. 2006 Apr 14;312(5771):212-7
16614208
Anal Chem. 2006 Aug 15;78(16):5678-84
16906711
BMC Bioinformatics. 2008 Jul 30;9:325
18664292
J Proteome Res. 2009 Jun;8(6):3176-81
19338334
Anal Chem. 2004 Jul 15;76(14):3908-22
15253624
Nat Biotechnol. 2004 Feb;22(2):214-9
14730315
J Proteome Res. 2007 May;6(5):1758-67
17397207