title: Evaluation of sample extraction methods for proteomics analysis of green algae Chlorella vulgaris.
abstract: Many protein extraction methods have been developed for plant proteome analysis but information is limited on the optimal protein extraction method from algae species. This study evaluated four protein extraction methods, i.e. direct lysis buffer method, TCA-acetone method, phenol method, and phenol/TCA-acetone method, using green algae Chlorella vulgaris for proteome analysis. The data presented showed that phenol/TCA-acetone method was superior to the other three tested methods with regards to shotgun proteomics. Proteins identified using shotgun proteomics were validated using sequential window acquisition of all theoretical fragment-ion spectra (SWATH) technique. Additionally, SWATH provides protein quantitation information from different methods and protein abundance using different protein extraction methods was evaluated. These results highlight the importance of green algae protein extraction method for subsequent MS analysis and identification.
authors.affiliation: Department of Chemistry, Faculty of Science, National University of Singapore, Singapore.
authors.forename: Yan
authors.initials: Y
authors.lastname: Gao
authors.affiliation: Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore.
authors.forename: Teck Kwang
authors.initials: TK
authors.lastname: Lim
authors.affiliation: Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore.|NUS Environmental Research Institute, National University of Singapore, Singapore.
authors.forename: Qingsong
authors.initials: Q
authors.lastname: Lin
authors.affiliation: Department of Chemistry, Faculty of Science, National University of Singapore, Singapore.|NUS Environmental Research Institute, National University of Singapore, Singapore.
authors.forename: Sam Fong Yau
authors.initials: SF
authors.lastname: Li
mesh_terms: D000096:Acetone / Q000737:chemistry; D002021:Buffers; D048408:Chlorella vulgaris / Q000737:chemistry* / Q000254:growth & development; D002851:Chromatography, High Pressure Liquid; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods; D013058:Mass Spectrometry; D019800:Phenol / Q000737:chemistry; D010940:Plant Proteins / Q000032:analysis* / Q000302:isolation & purification; D040901:Proteomics / Q000379:methods*
chemical_list: D002021:Buffers; D010940:Plant Proteins; D000096:Acetone; D019800:Phenol
keywords: Algae; Protein extraction; Sequential window acquisition of all theoretical fragment-ion spectra; Shotgun proteomics