title: Optimization of human dendritic cell sample preparation for mass spectrometry-based proteomic studies.
abstract: Dendritic cells (DCs) are specialized leukocytes that orchestrate the adaptive immune response. Mass spectrometry (MS)-based proteomic study of these cells presents technical challenges, especially when the DCs are human in origin due to the paucity of available biological material. Here, to maximize MS coverage of the global human DC proteome, different cell disruption methods, lysis conditions, protein precipitation, and protein pellet solubilization and denaturation methods were compared. Mechanical disruption of DC cell pellets under cryogenic conditions, coupled with the use of RIPA (radioimmunoprecipitation assay) buffer, was shown to be the method of choice based on total protein extraction and on the solubilization and identification of nuclear proteins. Precipitation by acetone was found to be more efficient than that by 10% trichloroacetic acid (TCA)/acetone, allowing in excess of 28% more protein identifications. Although being an effective strategy to eliminate the detergent residue, the acetone wash step caused a loss of protein identifications. However, this potential drawback was overcome by adding 1% sodium deoxycholate into the dissolution buffer, which enhanced both solubility of the precipitated proteins and digestion efficiency. This in turn resulted in 6 to 11% more distinct peptides and 14 to 19% more total proteins identified than using 0.5M triethylammonium bicarbonate alone, with the greatest increase (34%) for hydrophobic proteins.
authors.affiliation: Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland.
authors.forename: Ying
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland.
authors.forename: Dario
authors.initials: D
authors.lastname: Bottinelli
authors.affiliation: Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CH-1211 Geneva 4, Switzerland; Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland.
authors.forename: Frédérique
authors.initials: F
authors.lastname: Lisacek
authors.affiliation: Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Luban
authors.affiliation: Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors.forename: Caterina
authors.initials: C
authors.lastname: Strambio-De-Castillia
authors.affiliation: Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Varesio
authors.affiliation: Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland. Electronic address: gerard.hopfgartner@unige.ch.
authors.forename: Gérard
authors.initials: G
authors.lastname: Hopfgartner
mesh_terms: D000096:Acetone / Q000737:chemistry; D053000:Analytic Sample Preparation Methods / Q000379:methods*; D002021:Buffers; D011232:Chemical Precipitation; D003713:Dendritic Cells / Q000166:cytology / Q000378:metabolism*; D006801:Humans; D009000:Monocytes / Q000166:cytology; D017830:Octoxynol / Q000737:chemistry; D011489:Protein Denaturation; D021381:Protein Transport; D040901:Proteomics / Q000379:methods*; D015531:Radioimmunoprecipitation Assay; D012995:Solubility; D053719:Tandem Mass Spectrometry / Q000379:methods*; D014238:Trichloroacetic Acid / Q000737:chemistry
chemical_list: D002021:Buffers; D000096:Acetone; D014238:Trichloroacetic Acid; D017830:Octoxynol
keywords: LC–MS/MS; Monocyte-derived dendritic cells; Protein precipitation; Protein solubilization; Proteomics; Sample preparation