Proteotyping: Proteomic characterization, classification and identification of microorganisms--A prospectus.
Modern microbial systematics requires a range of methodologies for the comprehensive characterization, classification and identification of microorganisms. While whole-genome sequences provide the ultimate reference for defining microbial phylogeny and taxonomy, selected biomarker-based strategies continue to provide the means for the bulk of microbial systematic studies. Proteomics, the study of the expression of genes, as well as the structure and function of the resulting proteins, offers indirect measures of genome sequence data. Recent developments in applications of proteomics for analyzing microorganisms have paralleled the growing microbial genome sequence database, as well as the evolution of mass spectrometry (MS) instrumentation and bioinformatics. MALDI-TOF MS, which generates proteomic mass patterns for 'fingerprint'-based characterizations, has provided a marked breakthrough for microbial identification. However, MALDI-TOF MS is limited in the number of targets that can be detected for strain characterization. Advanced methods of tandem mass spectrometry, in which proteins and peptides generated from proteins, are characterized and identified, using LC-MS/MS, provide the ability to detect hundreds or thousands of expressed microbial strain markers for high-resolution characterizations and identifications. Model studies demonstrate the application of proteomics-based analyses for bacterial species- and strain-level detection and identification and for characterization of environmentally relevant, metabolically diverse bacteria. Proteomics-based approaches represent an emerging complement to traditional methods of characterizing microorganisms, enabling the elucidation of the expressed biomarkers of genome sequence information, which can be applied to 'proteotyping' applications of microorganisms at all taxonomic levels.
Department of Clinical Microbiology, Sahlgrenska University Hospital, SE-41346 Gothenburg, Sweden; Nanoxis Consulting AB, SE-40016 Gothenburg, Sweden. Electronic address: roger.karlsson@nanoxisconsulting.com.
Roger
R
Karlsson
Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, SE-40234 Gothenburg, Sweden.
Lucia
L
Gonzales-Siles
Department of Mathematical Sciences, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
Fredrik
F
Boulund
Department of Clinical Microbiology, Sahlgrenska University Hospital, SE-41346 Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, SE-40234 Gothenburg, Sweden.
Liselott
L
Svensson-Stadler
Department of Clinical Microbiology, Sahlgrenska University Hospital, SE-41346 Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, SE-40234 Gothenburg, Sweden.
Susann
S
Skovbjerg
Nanoxis Consulting AB, SE-40016 Gothenburg, Sweden.
Anders
A
Karlsson
Nanoxis Consulting AB, SE-40016 Gothenburg, Sweden.
Max
M
Davidson
Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296 Gothenburg, Sweden.
Stefan
S
Hulth
Department of Mathematical Sciences, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
Erik
E
Kristiansson
Department of Clinical Microbiology, Sahlgrenska University Hospital, SE-41346 Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, SE-40234 Gothenburg, Sweden; Culture Collection University of Gothenburg (CCUG), SE-41346 Gothenburg, Sweden.
Edward R B
ER
Moore
D001419:Bacteria / Q000737:chemistry / Q000145:classification; D001426:Bacterial Proteins / Q000032:analysis / Q000737:chemistry / Q000145:classification; D015373:Bacterial Typing Techniques; D013058:Mass Spectrometry; D020543:Proteome / Q000032:analysis / Q000737:chemistry / Q000145:classification; D040901:Proteomics
D001426:Bacterial Proteins; D020543:Proteome
Mass spectrometry; Microbial systematics; Proteomics; Proteotyping