title: Automated analysis of hemoglobin variants using nanoLC-MS and customized databases.
abstract: Unambiguous analysis of hemoglobin variants is critical in the diagnosis of hemoglobinopathies. In diagnostic laboratories, alkaline gel electrophoresis and automated HPLC are used in identifying variants. In specific instances, comigration of hemoglobin variant bands in gel and coelution of different variants or elution of variants with unmatched library information in HPLC can result in ambiguities in interpretation. Hemoglobin variants mostly arise from point mutations leading to very high sequence homology between normal and variant hemoglobin. In addition, unavailability of a variant database compatible with proteomics data analysis software makes mass spectrometry based variant analysis very challenging. In the present study, we standardized a nanoLC-MS based method for variant analysis to achieve substantially high sequence coverage. We developed three hemoglobin variant databases, specific to three different proteolytic enzymes, compatible with proteomics search engine software. The above nanoLC-MS method and the compatibility of the customized databases were validated by analysis of a sickle hemoglobin variant. Six other hemoglobin variants were characterized wherein diagnosis reports based on conventional tools were ambiguous. The novelty of our method lies in its simplicity and accuracy of the analysis with minimal manual intervention. The presently described method may be used in the future for the routine hemoglobin variant diagnosis.
authors.affiliation: Division of Molecular Medicine, Clinical Proteomics Unit, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore 560034, India.
authors.forename: Rajdeep
authors.initials: R
authors.lastname: Das
authors.forename: Gopa
authors.initials: G
authors.lastname: Mitra
authors.forename: Boby
authors.initials: B
authors.lastname: Mathew
authors.forename: Cecil
authors.initials: C
authors.lastname: Ross
authors.forename: Vijay
authors.initials: V
authors.lastname: Bhat
authors.forename: Amit Kumar
authors.initials: AK
authors.lastname: Mandal
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D002851:Chromatography, High Pressure Liquid; D030541:Databases, Genetic; D014644:Genetic Variation; D006453:Hemoglobinopathies / Q000175:diagnosis* / Q000235:genetics; D006454:Hemoglobins / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D013058:Mass Spectrometry; D009154:Mutation; D036103:Nanotechnology; D012984:Software
chemical_list: D006454:Hemoglobins