Comparison of detergent-based sample preparation workflows for LTQ-Orbitrap analysis of the Escherichia coli proteome
Articolo
Data di Pubblicazione:
2013
Citazione:
Comparison of detergent-based sample preparation workflows for LTQ-Orbitrap analysis of the Escherichia coli proteome / A. Tanca, G. Biosa, D. Pagnozzi, M.F. Addis, S. Uzzau. - In: PROTEOMICS. - ISSN 1615-9853. - 13:17(2013 Sep), pp. 2597-2607. [10.1002/pmic.201200478]
Abstract:
This work presents a comparative evaluation of several detergent-based sample preparation workflows for the MS-based analysis of bacterial proteomes, performed using the model organism Escherichia coli. Initially, RapiGest- and SDS-based buffers were compared for their protein extraction efficiency and quality of the MS data generated. As a result, SDS performed best in terms of total protein yields and overall number of MS identifications, mainly due to a higher efficiency in extracting high molecular weight (MW) and membrane proteins, while RapiGest led to an enrichment in periplasmic and fimbrial proteins. Then, SDS extracts underwent five different MS sample preparation workflows, including: detergent removal by spin columns followed by in-solution digestion (SC), protein precipitation followed by in-solution digestion in ammonium bicarbonate or urea buffer, filter-aided sample preparation (FASP), and 1DE separation followed by in-gel digestion. On the whole, about 1000 proteins were identified upon LC-MS/MS analysis of all preparations (>1100 with the SC workflow), with FASP producing more identified peptides and a higher mean sequence coverage. Each protocol exhibited specific behaviors in terms of MW, hydrophobicity, and subcellular localization distribution of the identified proteins; a comparative assessment of the different outputs is presented.
Tipologia IRIS:
01 - Articolo su periodico
Keywords:
FASP; Gram-negative bacteria; Microbiology; RapiGest; SDS; Shotgun proteomics; Chromatography, Liquid; Detergents; Escherichia coli; Escherichia coli Proteins; Membrane Proteins; Proteome; Proteomics; Specimen Handling; Tandem Mass Spectrometry; Workflow; Molecular Biology; Biochemistry
Elenco autori:
A. Tanca, G. Biosa, D. Pagnozzi, M.F. Addis, S. Uzzau
Link alla scheda completa: