DBParser: web-based software for shotgun proteomic data analyses.
We describe a web-based program called 'DBParser' for rapidly culling, merging, and comparing sequence search engine results from multiple LC-MS/MS peptide analyses. DBParser employs the principle of parsimony to consolidate redundant protein assignments and derive the most concise set of proteins consistent with all of the assigned peptide sequences observed in an experiment or series of experiments. The resulting reports summarize peptide and protein identifications from multidimensional experiments that may contain a single data set or combine data from a group of data sets, all related to a single analytical sample. Additionally, the results of multiple experiments, each of which may contain several data sets, can be compared in reports that identify features that are common or different. DBParser actively links to the primary mass spectral data and to public online databases such as NCBI, GO, and Swiss-Prot in order to structure contextually specific reports for biologists and biochemists.
Yang
Xiaoyu
X
National Institutes of Health, 10 Center Drive, Room 3D42, Bethesda, Maryland 20892-1262, USA.
Dondeti
Vijay
V
Dezube
Rebecca
R
Maynard
Dawn M
DM
Geer
Lewis Y
LY
Epstein
Jonathan
J
Chen
Xiongfong
X
Markey
Sanford P
SP
Kowalak
Jeffrey A
JA
D000595:Amino Acid Sequence; D002853:Chromatography, Liquid; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D010450:Endopeptidases / Q000378:metabolism; D020407:Internet; D013058:Mass Spectrometry / Q000379:methods; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000032:analysis; D011506:Proteins / Q000032:analysis* / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000737:chemistry; D012984:Software; D012985:Software Design; D012986:Software Validation; D021241:Spectrometry, Mass, Electrospray Ionization; D014584:User-Computer Interface
D010446:Peptide Fragments; D011506:Proteins; D010450:Endopeptidases