Electrophoretic Extraction and Proteomic Characterization of Proteins Buried in Marine Sediments
Abstract
:1. Introduction
2. Experimental Section
2.1. Sediment Collection
2.2. Gel Electrophoresis Protein Extraction
2.3. In Gel Protein Digestion
2.4. Direct Digestion of Sediment
2.5. Mass Spectrometry and Database Searching
2.6. Total Hydrolysable Amino Acid Analysis
3. Results and Discussion
Method | Protein (Annotation)/Peptides | Species | MW | Location | % |
---|---|---|---|---|---|
7 cm Tube Gel | RuBisCO large subunit | T. pseudonana | 54,324.7 | C | 13.3 |
(gi|118411104|ref|YP_874498.1|) | |||||
DTDVLALFR | |||||
FLNCLEGINR | |||||
MGYWDAAYTVK | |||||
MSGVDHIHAGTVVGK | |||||
VALEAMVLAR | |||||
YESGVIPYAK | |||||
Histone H4 | T. pseudonana | 11,383.6 | N | 43.7 | |
(jgi|Thaps3|3184|fgenesh1_pg.C_ chr_3000118) | |||||
DNIQGITKPAIR | |||||
ISGLIYEETR | |||||
VFLENVIR | |||||
VLRDNIQGITKPAIR | |||||
ATP-CF1-Beta | T. pseudonana | 51,143.1 | C | 5.3 | |
(gi|118411134|ref|YP_874528.1|) | |||||
FTQAGSEVSALLGR | |||||
IGLFGGAGVGK | |||||
P2A | T. pseudonana | 56,408.1 | C | 4.7 | |
(gi|118411113|ref|YP_874507.1|) | |||||
YQWDSGYFQQEIER | |||||
TSLESDGVFR | |||||
FCP-1 | T. pseudonana | 22,628.0 | C | 6.2 | |
(jgi|Thaps3|268127|estExt_thaps1_ ua_kg.C_chr_10394) | |||||
IAQLAFLGQVVTR | |||||
FCP-2 | T. pseudonana | 21,807.2 | C | 6.8 | |
(jgi|Thaps3|38667|e_gw1.22.164.1) | |||||
IAQLAFLGNIITR | |||||
FCP-3 | T. pseudonana | 20,354.4 | C | 6.8 | |
(jgi|Thaps3|38494|e_gw1.20.149.1) | |||||
ISQLAFLGQIVTR | |||||
P2-10P | T. pseudonana | 7,388.0 | C | 21.2 | |
(gi|118411116|ref|YP_874510.1|) | |||||
LGEILRPLNAEYGK | |||||
Putative cysteine synthase | T. pseudonana | 37,867.3 | M | 4.6 | |
(jgi|Thaps3|38294|e_gw1.19a.45.1) | |||||
MENLNPGGTGKDRAAR | |||||
DNA-RNA-P-Gamma | P. marinus | 72,277.0 | S | 1.7 | |
(gi|33862040|ref|NP_893601.1|) | |||||
FATSDLNDLYR | |||||
ATP-PBS | P. marinus | 49,496.0 | S | 3.1 | |
(gi|33862213|ref|NP_893774.1|) | |||||
DVSGEGVQQALLK | |||||
2 cm Tube Gel | FCP-2 | T. pseudonana | 21,807.2 | C | 7.3 |
(jgi|Thaps3|38667|e_gw1.22.164.1) | |||||
DIEGTGNEFVGDFR | |||||
P2RC-D2 | T. pseudonana | 39,064.0 | C | 3.7 | |
(gi|118411148|ref|YP_874542.1|) | |||||
AAEDPEFETFYTK | |||||
H-DNA-BP | P. marinus | 9,768.0 | S | 24.2 | |
(gi|33861877|ref|NP_893438.1|) | |||||
TDVSLVVDAAIETIVDSVVEGK | |||||
1D Gel | H-DNA-BP | P. marinus | 9,768.0 | S | 24.2 |
(gi|33861877|ref|NP_893438.1|) | |||||
TDVSLVVDAAIETIVDSVVEGK | |||||
DD | H-DNA-BP | P. marinus | 9,768.0 | S | 24.2 |
(gi|33861877|ref|NP_893438.1|) | |||||
TDVSLVVDAAIETIVDSVVEGK |
Gel Section (kDa) | Protein/Peptides | Species | MW | CL | % |
---|---|---|---|---|---|
>100 | RuBisCO large subunit | T. pseudonana | 54,324.7 | C | 7.1 |
MSGVDHIHAGTVVGK | |||||
VALEAMVLAR | |||||
FLNCLEGINR | |||||
Histone H4 | T. pseudonana | 11,383.6 | N | 22.3 | |
DNIQGITKPAIR | |||||
VFLENVIR | |||||
VLRDNIQGITKPAIR | |||||
FCP-2 | T. pseudonana | 21,807.2 | C | 6.8 | |
IAQLAFLGNIITR | |||||
ATP-CF1-Beta | T. pseudonana | 51,143.1 | C | 3.0 | |
FTQAGSEVSALLGR | |||||
Putative cysteine synthase | T. pseudonana | 37,867.3 | M | 4.6 | |
MENLNPGGTGKDRAAR | |||||
DNA-RNA-P-Gamma | P. marinus | 72,277.0 | S | 1.7 | |
FATSDLNDLYR | |||||
ATP-PBS | P. marinus | 49,496.0 | S | 3.1 | |
DVSGEGVQQALLK | |||||
50 to 100 | RuBisCO large subunit | T. pseudonana | 54,324.7 | C | 9.2 |
DTDVLALFR | |||||
MSGVDHIHAGTVVGK | |||||
YESGVIPYAK | |||||
MGYWDAAYTVK | |||||
Histone H4 | T. pseudonana | 11,383.6 | N | 21.4 | |
ISGLIYEETR | |||||
DNIQGITKPAIR | |||||
ATP-CF1-Beta | T. pseudonana | 51,143.1 | C | 3.0 | |
FTQAGSEVSALLGR | |||||
FCP-2 | T. pseudonana | 21,807.2 | C | 6.8 | |
IAQLAFLGNIITR | |||||
25 to 50 | Histone H4 | T. pseudonana | 11,383.6 | N | 17.5 |
ISGLIYEETR | |||||
VFLENVIR | |||||
P2A | T. pseudonana | 56,408.1 | C | 4.7 | |
YQWDSGYFQQEIER | |||||
TSLESDGVFR | |||||
ATP-CF1-Beta | T. pseudonana | 51,143.1 | C | 3.0 | |
FTQAGSEVSALLGR | |||||
FCP-2 | T. pseudonana | 21,807.2 | C | 6.8 | |
IAQLAFLGNIITR | |||||
P2-10P | T. pseudonana | 7,388.0 | C | 21.2 | |
LGEILRPLNAEYGK | |||||
10 to 25 | P2-10P | T. pseudonana | 7,388.0 | C | 21.2 |
LGEILRPLNAEYGK | |||||
Histone H4 | T. pseudonana | 11,383.6 | N | 29.1 | |
ISGLIYEETR | |||||
VFLENVIR | |||||
DNIQGITKPAIR | |||||
ATP-CF1-Beta | T. pseudonana | 51,143.1 | C | 5.3 | |
IGLFGGAGVGK | |||||
FTQAGSEVSALLGR | |||||
FCP-1 | T. pseudonana | 22,628.0 | C | 6.2 | |
IAQLAFLGQVVTR | |||||
FCP-2 | T. pseudonana | 21,807.2 | C | 6.8 | |
IAQLAFLGNIITR | |||||
FCP-3 | T. pseudonana | 20,354.4 | C | 6.8 | |
ISQLAFLGQIVTR | |||||
<10 | no IDs |
4. Conclusions
Supplemental Information
Acknowledgments
Author Contributions
Conflicts of Interest
References and Notes
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Moore, E.K.; Harvey, H.R.; Faux, J.F.; Goodlett, D.R.; Nunn, B.L. Electrophoretic Extraction and Proteomic Characterization of Proteins Buried in Marine Sediments. Chromatography 2014, 1, 176-193. https://doi.org/10.3390/chromatography1040176
Moore EK, Harvey HR, Faux JF, Goodlett DR, Nunn BL. Electrophoretic Extraction and Proteomic Characterization of Proteins Buried in Marine Sediments. Chromatography. 2014; 1(4):176-193. https://doi.org/10.3390/chromatography1040176
Chicago/Turabian StyleMoore, Eli K., H. Rodger Harvey, Jessica F. Faux, David R. Goodlett, and Brook L. Nunn. 2014. "Electrophoretic Extraction and Proteomic Characterization of Proteins Buried in Marine Sediments" Chromatography 1, no. 4: 176-193. https://doi.org/10.3390/chromatography1040176
APA StyleMoore, E. K., Harvey, H. R., Faux, J. F., Goodlett, D. R., & Nunn, B. L. (2014). Electrophoretic Extraction and Proteomic Characterization of Proteins Buried in Marine Sediments. Chromatography, 1(4), 176-193. https://doi.org/10.3390/chromatography1040176