In-Depth Analysis of Exoproteomes from Marine Bacteria by Shotgun Liquid Chromatography-Tandem Mass Spectrometry: the Ruegeria pomeroyi DSS-3 Case-Study
Abstract
:1. Introduction
2. Results and Discussion
2.1. A shotgun nano-LC-MS/MS strategy for a comprehensive exoproteome
2.2. A broad exoproteome is revealed in a one-shot analysis
2.3. Confirmation of the nature and over-representation of the most abundant proteins
2.4. Structural and functional hints regarding YP_165496
2.5. Structure and role of the two other major secreted proteins
2.7. Other proteins identified with a signal peptide
3. Experimental
3.1. Exoproteome samples
3.2. Trypsin in-gel proteolysis and nano-LC-MS/MS analysis
3.3. MS/MS database search
3.4. Protein quantification
3.5. Protein and nucleic sequence analysis
4. Conclusions
Acknowledgements
- Samples Availability: Available from the authors.
References
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Accession | Function | # peptides | # MS/MS | Signal Peptide prediction |
---|---|---|---|---|
Most abundant proteins detected | ||||
YP_165496 | PaxA, putative | 45 | 2610 | absence |
YP_165625 | type I secretion target repeat-containing protein | 48 | 359 | absence |
YP_168868 | type I secretion target repeat-containing protein | 37 | 164 | absence |
Proteins ABC and TRAP transporters | ||||
YP_168968 | oligopeptide/dipeptide ABC transporter, periplasmic | 13 | 58 | presence |
YP_168022 | peptide/opine/nickel uptake ABC transporter periplasmic | 16 | 54 | presence |
YP_168201 | peptide/nickel/opine uptake ABC transporter periplasmic | 10 | 42 | presence * |
YP_165781 | glutamate/glutamine/aspartate/asparagine ABC transporter, periplasmic | 10 | 39 | presence * |
YP_168669 | polyamine ABC trasnporter, periplasmic polyamine-binding protein | 6 | 28 | presence |
YP_165868 | sugar ABC transporter, periplasmic sugar-binding protein | 7 | 24 | presence |
YP_167838 | TRAP transporter solute receptor DctP family protein | 6 | 19 | presence |
YP_167174 | branched-chain amino acid ABC transporter, periplasmic | 4 | 14 | presence |
YP_167412 | TRAP transporter solute receptor TAXI family protein | 5 | 13 | presence |
YP_165067 | TRAP dicarboxylate transporter, DctP subunit | 4 | 13 | presence |
YP_165642 | sugar ABC transporter, periplasmic sugar-binding protein | 3 | 12 | presence |
YP_166898 | oligopeptide/dipeptide ABC transporter, periplasmic | 2 | 10 | presence * |
YP_166382 | glycine betaine/proline ABC transporter, periplasmic | 2 | 5 | presence |
YP_165960 | oligopeptide ABC transporter, periplasmic | 3 | 4 | presence |
YP_166114 | xylose ABC transporter, periplasmic xylose-binding protein | 2 | 2 | presence |
YP_167025 | ABC transporter, periplasmic substrate-binding protein | 2 | 2 | presence |
Other proteins with predicted signal peptide | ||||
YP_165456 | hypothetical protein SPO0186 | 10 | 37 | presence |
YP_167495 | 3-oxoacyl-(acyl carrier protein) synthase II | 4 | 21 | presence |
YP_167459 | peptidyl-prolyl cis-trans isomerase, cyclophilin-type | 6 | 20 | presence |
YP_165903 | bmp family protein | 4 | 14 | presence |
YP_165402 | cytochrome c family protein | 4 | 12 | presence |
YP_165589 | acetyl-CoA acetyltransferase | 4 | 9 | presence |
YP_168626 | outer membrane porin | 3 | 7 | presence |
YP_167817 | solute-binding family 7 protein | 2 | 5 | presence |
YP_167786 | solute-binding family 7 protein | 3 | 4 | presence |
YP_167503 | hypothetical protein SPO2279 | 2 | 4 | presence |
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Christie-Oleza, J.A.; Armengaud, J. In-Depth Analysis of Exoproteomes from Marine Bacteria by Shotgun Liquid Chromatography-Tandem Mass Spectrometry: the Ruegeria pomeroyi DSS-3 Case-Study. Mar. Drugs 2010, 8, 2223-2239. https://doi.org/10.3390/md8082223
Christie-Oleza JA, Armengaud J. In-Depth Analysis of Exoproteomes from Marine Bacteria by Shotgun Liquid Chromatography-Tandem Mass Spectrometry: the Ruegeria pomeroyi DSS-3 Case-Study. Marine Drugs. 2010; 8(8):2223-2239. https://doi.org/10.3390/md8082223
Chicago/Turabian StyleChristie-Oleza, Joseph Alexander, and Jean Armengaud. 2010. "In-Depth Analysis of Exoproteomes from Marine Bacteria by Shotgun Liquid Chromatography-Tandem Mass Spectrometry: the Ruegeria pomeroyi DSS-3 Case-Study" Marine Drugs 8, no. 8: 2223-2239. https://doi.org/10.3390/md8082223