title: Protein-Sequence Polymorphisms and Post-translational Modifications in Proteins from Human Saliva using Top-Down Fourier-transform Ion Cyclotron Resonance Mass Spectrometry.
abstract: Single nucleotide polymorphisms (SNPs) can result in protein sequence polymorphisms (PSPs) when codon translations are altered. Both top-down and bottom-up proteomics strategies can identify PSPs, but only if databases and software are used with this in mind. A 14319 Da protein from human saliva was characterized using the top-down approach on a hybrid linear ion-trap Fourier-transform ion cyclotron resonance mass spectrometer equipped for both collisionally-activated (CAD) and electron-capture (ECD) dissociation. Sequence tags identified the protein as Cystatin SN, and defined the N-terminal signal peptide cleavage site, as well as two disulfide bonds, in agreement with previous studies. The mass of the intact protein (< 5 ppm error) deviated from that calculated from the published gene sequence by 16.031 Da, and, based on CAD and ECD fragment ion assignments, it was concluded that the isoform of the protein analyzed carried a PSP at residue 11 such that the Pro translated from the genome was in fact Leu/Ile. An independently determined SNP (rs2070856) subsequently confirmed the genetic basis of the mass spectral interpretation and defined the residue as Leu. In another example, the PRP3 protein with mass ∼10,999 Da was found to be an isomeric/isobaric mixture of the reported sequence with PSPs D4N or D50N (rs1049112). Both CAD and ECD datasets support two phosphorylation sites at residues Ser8 and Ser22, rather than Ser17. In the context of discovery proteomics, previously undefined PSPs and PTMs will only be detected if the logic of data processing strategies considers their presence in an unbiased fashion.
authors.affiliation: The Pasarow Mass Spectrometry Laboratory, NPI - Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, 760 West wood Plaza, Los Angeles, CA 90024.
authors.forename: Julian P
authors.initials: JP
authors.lastname: Whitelegge
authors.forename: Vlad
authors.initials: V
authors.lastname: Zabrouskov
authors.forename: Frederic
authors.initials: F
authors.lastname: Halgand
authors.forename: Puneet
authors.initials: P
authors.lastname: Souda
authors.forename: Sara
authors.initials: S
authors.lastname: Bassilian
authors.forename: Weihong
authors.initials: W
authors.lastname: Yan
authors.forename: Larry
authors.initials: L
authors.lastname: Wolinsky
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Loo
authors.forename: David T W
authors.initials: DT
authors.lastname: Wong
authors.forename: Kym F
authors.initials: KF
authors.lastname: Faull