title: Sensitive and specific identification of wild type and variant proteins from 8 to 669 kDa using top-down mass spectrometry.
abstract: Top-down and bottom-up mass spectrometry methods can generate gas phase fragments and use these to identify proteins. Top-down methods, in addition, can provide the mass of the protein itself and therefore additional structural information. Despite the conceptual advantage of top-down methods, the market share advantage belongs to bottom-up methods as a result of their more robust sample preparation, fragmentation, and data processing methods. Here we report improved fragmentation and data processing methods for top-down mass spectrometry. Specifically we report the use of funnel-skimmer dissociation, a variation of nozzle-skimmer dissociation, and compare its performance with electron capture dissociation. We also debut BIG Mascot, an extended version of Mascot with incorporated top-down MS(2) search ability and the first search engine that can perform both bottom-up and top-down searches. Using BIG Mascot, we demonstrated the ability to identify proteins 1) using only intact protein MS(1), 2) using only MS(2), and 3) using the combination of MS(1) and MS(2). We correctly identified proteins with a wide range of masses, including 13 amyotrophic lateral sclerosis-associated variants of the protein Cu/Zn-superoxide dismutase, and extended the upper mass limit of top-down protein identification to 669 kDa by identifying thyroglobulin.
authors.affiliation: Department of Chemistry and Volen Center for Complex Systems, National Center of Behavioral Genomics, Brandeis University, Waltham, Massachusetts 02454, USA.
authors.forename: N Murat
authors.initials: NM
authors.lastname: Karabacak
authors.forename: Long
authors.initials: L
authors.lastname: Li
authors.forename: Ashutosh
authors.initials: A
authors.lastname: Tiwari
authors.forename: Lawrence J
authors.initials: LJ
authors.lastname: Hayward
authors.forename: Pengyu
authors.initials: P
authors.lastname: Hong
authors.forename: Michael L
authors.initials: ML
authors.lastname: Easterling
authors.forename: Jeffrey N
authors.initials: JN
authors.lastname: Agar
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D002417:Cattle; D030562:Databases, Protein; D006736:Horses; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D008970:Molecular Weight; D050505:Mutant Proteins / Q000032:analysis* / Q000737:chemistry*; D012680:Sensitivity and Specificity; D012997:Solvents; D013482:Superoxide Dismutase / Q000737:chemistry; D013954:Thyroglobulin / Q000737:chemistry
chemical_list: D050505:Mutant Proteins; D012997:Solvents; D013954:Thyroglobulin; D013482:Superoxide Dismutase