Meta sequence analysis of human blood peptides and their parent proteins.
Sequence analysis of the blood peptides and their qualities will be key to understanding the mechanisms that contribute to error in LC-ESI-MS/MS. Analysis of peptides and their proteins at the level of sequences is much more direct and informative than the comparison of disparate accession numbers. A portable database of all blood peptide and protein sequences with descriptor fields and gene ontology terms might be useful for designing immunological or MRM assays from human blood. The results of twelve studies of human blood peptides and/or proteins identified by LC-MS/MS and correlated against a disparate array of genetic libraries were parsed and matched to proteins from the human ENSEMBL, SwissProt and RefSeq databases by SQL. The reported peptide and protein sequences were organized into an SQL database with full protein sequences and up to five unique peptides in order of prevalence along with the peptide count for each protein. Structured query language or BLAST was used to acquire descriptive information in current databases. Sampling error at the level of peptides is the largest source of disparity between groups. Chi Square analysis of peptide to protein distributions confirmed the significant agreement between groups on identified proteins.
Bowden
Peter
P
Department of Chemistry and Biology, Ryerson University, Toronto, Canada.
Pendrak
Voitek
V
Zhu
Peihong
P
Marshall
John G
JG
D000465:Algorithms; D001798:Blood Proteins / Q000737:chemistry*; D002853:Chromatography, Liquid / Q000379:methods; D005188:False Negative Reactions; D005189:False Positive Reactions; D006801:Humans; D015233:Models, Statistical; D010455:Peptides / Q000737:chemistry; D011506:Proteins / Q000737:chemistry; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods; D053719:Tandem Mass Spectrometry / Q000379:methods; D014357:Trypsin / Q000737:chemistry
D001798:Blood Proteins; D010455:Peptides; D011506:Proteins; D020543:Proteome; D014357:Trypsin