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ProMEX - a mass spectral reference database for plant proteomics.

Wienkoop S, Staudinger C, Hoehenwarter W, Weckwerth W, Egelhofer V - Front Plant Sci (2012)

Bottom Line: The ProMEX database is one of the main collection of annotated tryptic peptides in plant proteomics.The main objective of the ProMEX database is to provide experimental MS/MS-based information for cell type-specific or sub-cellular proteomes in Arabidopsis thaliana, Medicago truncatula, Chlamydomonas reinhardtii, Lotus japonicus, Lotus corniculatus, Phaseolus vulgaris, Lycopersicon esculentum, Solanum tuberosum, Nicotiana tabacum, Glycine max, Zea mays, Bradyrhizobium japonicum, and Sinorhizobium meliloti.Direct links at the protein level to the most relevant databases are present in ProMEX.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Systems Biology, University of Vienna, Vienna, Austria.

ABSTRACT
The ProMEX database is one of the main collection of annotated tryptic peptides in plant proteomics. The main objective of the ProMEX database is to provide experimental MS/MS-based information for cell type-specific or sub-cellular proteomes in Arabidopsis thaliana, Medicago truncatula, Chlamydomonas reinhardtii, Lotus japonicus, Lotus corniculatus, Phaseolus vulgaris, Lycopersicon esculentum, Solanum tuberosum, Nicotiana tabacum, Glycine max, Zea mays, Bradyrhizobium japonicum, and Sinorhizobium meliloti. Direct links at the protein level to the most relevant databases are present in ProMEX. Furthermore, the spectral sequence information are linked to their respective pathways and can be viewed in pathway maps.

No MeSH data available.


Related in: MedlinePlus

MS/MS spectrum of peptide DLVALSGAHTIGQAR with precursor mass at 754.915. The dominant fragments ions (b, y) are labeled. The experimental conditions are shown below the spectrum.
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Figure 1: MS/MS spectrum of peptide DLVALSGAHTIGQAR with precursor mass at 754.915. The dominant fragments ions (b, y) are labeled. The experimental conditions are shown below the spectrum.

Mentions: Previously identified high quality spectra provide information about sequence coverage as well as missing sequence information. The sequence coverage may give semi-quantitative information about the abundance of a protein or peptide while missing peptide sequences could provide important information about unknown modifications. In addition, the most common post-translational modifications such as oxidation and phosphorylation are indicated, if present. Moreover, the peptide fragment ions indicated by a, b, c, x, y, or z can be visualized to get an impression of the quality of the displayed spectra (Figure 1).


ProMEX - a mass spectral reference database for plant proteomics.

Wienkoop S, Staudinger C, Hoehenwarter W, Weckwerth W, Egelhofer V - Front Plant Sci (2012)

MS/MS spectrum of peptide DLVALSGAHTIGQAR with precursor mass at 754.915. The dominant fragments ions (b, y) are labeled. The experimental conditions are shown below the spectrum.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3368217&req=5

Figure 1: MS/MS spectrum of peptide DLVALSGAHTIGQAR with precursor mass at 754.915. The dominant fragments ions (b, y) are labeled. The experimental conditions are shown below the spectrum.
Mentions: Previously identified high quality spectra provide information about sequence coverage as well as missing sequence information. The sequence coverage may give semi-quantitative information about the abundance of a protein or peptide while missing peptide sequences could provide important information about unknown modifications. In addition, the most common post-translational modifications such as oxidation and phosphorylation are indicated, if present. Moreover, the peptide fragment ions indicated by a, b, c, x, y, or z can be visualized to get an impression of the quality of the displayed spectra (Figure 1).

Bottom Line: The ProMEX database is one of the main collection of annotated tryptic peptides in plant proteomics.The main objective of the ProMEX database is to provide experimental MS/MS-based information for cell type-specific or sub-cellular proteomes in Arabidopsis thaliana, Medicago truncatula, Chlamydomonas reinhardtii, Lotus japonicus, Lotus corniculatus, Phaseolus vulgaris, Lycopersicon esculentum, Solanum tuberosum, Nicotiana tabacum, Glycine max, Zea mays, Bradyrhizobium japonicum, and Sinorhizobium meliloti.Direct links at the protein level to the most relevant databases are present in ProMEX.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Systems Biology, University of Vienna, Vienna, Austria.

ABSTRACT
The ProMEX database is one of the main collection of annotated tryptic peptides in plant proteomics. The main objective of the ProMEX database is to provide experimental MS/MS-based information for cell type-specific or sub-cellular proteomes in Arabidopsis thaliana, Medicago truncatula, Chlamydomonas reinhardtii, Lotus japonicus, Lotus corniculatus, Phaseolus vulgaris, Lycopersicon esculentum, Solanum tuberosum, Nicotiana tabacum, Glycine max, Zea mays, Bradyrhizobium japonicum, and Sinorhizobium meliloti. Direct links at the protein level to the most relevant databases are present in ProMEX. Furthermore, the spectral sequence information are linked to their respective pathways and can be viewed in pathway maps.

No MeSH data available.


Related in: MedlinePlus