A comparison of labeling and label-free mass spectrometry-based proteomics approaches.
The proteome of the recently discovered bacterium Methylocella silvestris has been characterized using three profiling and comparative proteomics approaches. The organism has been grown on two different substrates enabling variations in protein expression to be identified. The results obtained using the experimental approaches have been compared with respect to number of proteins identified, confidence in identification, sequence coverage and agreement of regulated proteins. The sample preparation, instrumental time and sample loading requirements of the differing experiments are compared and discussed. A preliminary screen of the protein regulation results for biological significance has also been performed.
Patel
Vibhuti J
VJ
Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom.
Thalassinos
Konstantinos
K
Slade
Susan E
SE
Connolly
Joanne B
JB
Crombie
Andrew
A
Murrell
J Colin
JC
Scrivens
James H
JH
D000465:Algorithms; D001331:Automation; D001419:Bacteria / Q000378:metabolism*; D001426:Bacterial Proteins / Q000737:chemistry; D015415:Biomarkers / Q000737:chemistry; D002853:Chromatography, Liquid / Q000379:methods; D030562:Databases, Protein; D004591:Electrophoresis, Polyacrylamide Gel; D013058:Mass Spectrometry / Q000379:methods*; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000737:chemistry; D020543:Proteome / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D013194:Staining and Labeling; D014357:Trypsin / Q000737:chemistry
D001426:Bacterial Proteins; D015415:Biomarkers; D011506:Proteins; D020543:Proteome; D014357:Trypsin