Shotgun proteomic analysis of a chromatophore-enriched preparation from the purple phototrophic bacterium Rhodopseudomonas palustris View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2003-12

AUTHORS

Anthony P. Fejes, Eugene C. Yi, David R. Goodlett, J. Thomas Beatty

ABSTRACT

A proteomics approach was evaluated for analysis of photosyntheis-related proteins that are characteristic of chromatophores, particles derived from purple phototrophic bacterial intracytoplasmic membranes. Proteins of purified chromatophores from Rhodopseudomonas palustris were solubilized and digested with trypsin, to create a collection of peptides that were fractionated by liquid chromatography. Peptide sequences were determined and assigned to specific proteins by analysis of tandem mass spectra of peptides, and comparison to a library derived from the recently determined R. palustris genome sequence. A total of 300 proteins were detected with a probability value ≥0.9, and the number of proteins detected increased to 345 when the minimum probability value was reduced to 0.5. Membrane–integral proteins of the reaction center, cytochrome b/c1, light-harvesting and ATPase complexes were used as controls to assess how well this approach performs with hydrophobic proteins. New genes were identified, and tentatively designated as encoding photosynthesis-related proteins. We conclude that this approach is a powerful method to evaluate the possible existence of new photosynthesis-related proteins (and genes), although alternative methods are needed to evaluate the exact functions of newly discovered genes. More... »

PAGES

195-203

Identifiers

URI

http://scigraph.springernature.com/pub.10.1023/b:pres.0000006752.81486.74

DOI

http://dx.doi.org/10.1023/b:pres.0000006752.81486.74

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1021746993

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/16245051


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0601", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biochemistry and Cell Biology", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Department of Microbiology and Immunology, University of British Columbia, V6T 1Z3, Vancouver, BC, Canada", 
          "id": "http://www.grid.ac/institutes/grid.17091.3e", 
          "name": [
            "Department of Microbiology and Immunology, University of British Columbia, V6T 1Z3, Vancouver, BC, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Fejes", 
        "givenName": "Anthony P.", 
        "id": "sg:person.0672053321.72", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0672053321.72"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "The Institute for Systems Biology, 98103, Seattle, WA, USA", 
          "id": "http://www.grid.ac/institutes/grid.64212.33", 
          "name": [
            "The Institute for Systems Biology, 98103, Seattle, WA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Yi", 
        "givenName": "Eugene C.", 
        "id": "sg:person.01064603366.33", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01064603366.33"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "The Institute for Systems Biology, 98103, Seattle, WA, USA", 
          "id": "http://www.grid.ac/institutes/grid.64212.33", 
          "name": [
            "The Institute for Systems Biology, 98103, Seattle, WA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Goodlett", 
        "givenName": "David R.", 
        "id": "sg:person.01044126157.13", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01044126157.13"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Microbiology and Immunology, University of British Columbia, V6T 1Z3, Vancouver, BC, Canada", 
          "id": "http://www.grid.ac/institutes/grid.17091.3e", 
          "name": [
            "Department of Microbiology and Immunology, University of British Columbia, V6T 1Z3, Vancouver, BC, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Beatty", 
        "givenName": "J. Thomas", 
        "id": "sg:person.0603657647.00", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0603657647.00"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1007/0-306-47954-0_12", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031827688", 
          "https://doi.org/10.1007/0-306-47954-0_12"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1016/1044-0305(94)80016-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018629105", 
          "https://doi.org/10.1016/1044-0305(94)80016-2"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/0-306-47954-0_44", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041874390", 
          "https://doi.org/10.1007/0-306-47954-0_44"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/0-306-47954-0_34", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030117726", 
          "https://doi.org/10.1007/0-306-47954-0_34"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/10890", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012772847", 
          "https://doi.org/10.1038/10890"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1023/a:1016132700844", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025875146", 
          "https://doi.org/10.1023/a:1016132700844"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2003-12", 
    "datePublishedReg": "2003-12-01", 
    "description": "A proteomics approach was evaluated for analysis of photosyntheis-related proteins that are characteristic of chromatophores, particles derived from purple phototrophic bacterial intracytoplasmic membranes. Proteins of purified chromatophores from Rhodopseudomonas palustris were solubilized and digested with trypsin, to create a collection of peptides that were fractionated by liquid chromatography. Peptide sequences were determined and assigned to specific proteins by analysis of tandem mass spectra of peptides, and comparison to a library derived from the recently determined R. palustris genome sequence. A total of 300 proteins were detected with a probability value \u22650.9, and the number of proteins detected increased to 345 when the minimum probability value was reduced to 0.5. Membrane\u2013integral proteins of the reaction center, cytochrome b/c1, light-harvesting and ATPase complexes were used as controls to assess how well this approach performs with hydrophobic proteins. New genes were identified, and tentatively designated as encoding photosynthesis-related proteins. We conclude that this approach is a powerful method to evaluate the possible existence of new photosynthesis-related proteins (and genes), although alternative methods are needed to evaluate the exact functions of newly discovered genes.", 
    "genre": "article", 
    "id": "sg:pub.10.1023/b:pres.0000006752.81486.74", 
    "isAccessibleForFree": false, 
    "isPartOf": [
      {
        "id": "sg:journal.1022986", 
        "issn": [
          "0166-8595", 
          "1573-5079"
        ], 
        "name": "Photosynthesis Research", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "3", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "78"
      }
    ], 
    "keywords": [
      "photosynthesis-related proteins", 
      "Rhodopseudomonas palustris", 
      "membrane integral proteins", 
      "shotgun proteomic analysis", 
      "phototrophic bacterium Rhodopseudomonas palustris", 
      "number of proteins", 
      "bacterium Rhodopseudomonas palustris", 
      "new genes", 
      "proteomic approach", 
      "collection of peptides", 
      "genome sequence", 
      "proteomic analysis", 
      "hydrophobic proteins", 
      "ATPase complex", 
      "intracytoplasmic membranes", 
      "specific proteins", 
      "exact function", 
      "tandem mass spectra", 
      "protein", 
      "mass spectra", 
      "peptide sequences", 
      "genes", 
      "reaction centers", 
      "palustris", 
      "liquid chromatography", 
      "enriched preparation", 
      "chromatophores", 
      "sequence", 
      "peptides", 
      "powerful method", 
      "chromatography", 
      "membrane", 
      "trypsin", 
      "complexes", 
      "preparation", 
      "possible existence", 
      "library", 
      "spectra", 
      "particles", 
      "analysis", 
      "function", 
      "C1", 
      "alternative method", 
      "method", 
      "number", 
      "collection", 
      "values", 
      "control", 
      "approach", 
      "existence", 
      "total", 
      "comparison", 
      "probability values", 
      "center"
    ], 
    "name": "Shotgun proteomic analysis of a chromatophore-enriched preparation from the purple phototrophic bacterium Rhodopseudomonas palustris", 
    "pagination": "195-203", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1021746993"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1023/b:pres.0000006752.81486.74"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "16245051"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1023/b:pres.0000006752.81486.74", 
      "https://app.dimensions.ai/details/publication/pub.1021746993"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2022-11-24T20:50", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20221124/entities/gbq_results/article/article_369.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1023/b:pres.0000006752.81486.74"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1023/b:pres.0000006752.81486.74'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1023/b:pres.0000006752.81486.74'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1023/b:pres.0000006752.81486.74'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1023/b:pres.0000006752.81486.74'


 

This table displays all metadata directly associated to this object as RDF triples.

163 TRIPLES      21 PREDICATES      86 URIs      72 LITERALS      7 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1023/b:pres.0000006752.81486.74 schema:about anzsrc-for:06
2 anzsrc-for:0601
3 schema:author N03e78326aaf341fbadfa9ba24c4fa0b2
4 schema:citation sg:pub.10.1007/0-306-47954-0_12
5 sg:pub.10.1007/0-306-47954-0_34
6 sg:pub.10.1007/0-306-47954-0_44
7 sg:pub.10.1016/1044-0305(94)80016-2
8 sg:pub.10.1023/a:1016132700844
9 sg:pub.10.1038/10890
10 schema:datePublished 2003-12
11 schema:datePublishedReg 2003-12-01
12 schema:description A proteomics approach was evaluated for analysis of photosyntheis-related proteins that are characteristic of chromatophores, particles derived from purple phototrophic bacterial intracytoplasmic membranes. Proteins of purified chromatophores from Rhodopseudomonas palustris were solubilized and digested with trypsin, to create a collection of peptides that were fractionated by liquid chromatography. Peptide sequences were determined and assigned to specific proteins by analysis of tandem mass spectra of peptides, and comparison to a library derived from the recently determined R. palustris genome sequence. A total of 300 proteins were detected with a probability value ≥0.9, and the number of proteins detected increased to 345 when the minimum probability value was reduced to 0.5. Membrane–integral proteins of the reaction center, cytochrome b/c1, light-harvesting and ATPase complexes were used as controls to assess how well this approach performs with hydrophobic proteins. New genes were identified, and tentatively designated as encoding photosynthesis-related proteins. We conclude that this approach is a powerful method to evaluate the possible existence of new photosynthesis-related proteins (and genes), although alternative methods are needed to evaluate the exact functions of newly discovered genes.
13 schema:genre article
14 schema:isAccessibleForFree false
15 schema:isPartOf Neee02a0a3f044129a91bf862385c8d62
16 Nfc9a0801b0254d5a8f31f45ccceab1a0
17 sg:journal.1022986
18 schema:keywords ATPase complex
19 C1
20 Rhodopseudomonas palustris
21 alternative method
22 analysis
23 approach
24 bacterium Rhodopseudomonas palustris
25 center
26 chromatography
27 chromatophores
28 collection
29 collection of peptides
30 comparison
31 complexes
32 control
33 enriched preparation
34 exact function
35 existence
36 function
37 genes
38 genome sequence
39 hydrophobic proteins
40 intracytoplasmic membranes
41 library
42 liquid chromatography
43 mass spectra
44 membrane
45 membrane integral proteins
46 method
47 new genes
48 number
49 number of proteins
50 palustris
51 particles
52 peptide sequences
53 peptides
54 photosynthesis-related proteins
55 phototrophic bacterium Rhodopseudomonas palustris
56 possible existence
57 powerful method
58 preparation
59 probability values
60 protein
61 proteomic analysis
62 proteomic approach
63 reaction centers
64 sequence
65 shotgun proteomic analysis
66 specific proteins
67 spectra
68 tandem mass spectra
69 total
70 trypsin
71 values
72 schema:name Shotgun proteomic analysis of a chromatophore-enriched preparation from the purple phototrophic bacterium Rhodopseudomonas palustris
73 schema:pagination 195-203
74 schema:productId N14d7da2f4e9340d1b63e1d14a8873955
75 Nb787d8cf9214456c844f609c863b2114
76 Nbed8a73398d448cebe0091f203069041
77 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021746993
78 https://doi.org/10.1023/b:pres.0000006752.81486.74
79 schema:sdDatePublished 2022-11-24T20:50
80 schema:sdLicense https://scigraph.springernature.com/explorer/license/
81 schema:sdPublisher Naae18def8398422aade88e1693cfc552
82 schema:url https://doi.org/10.1023/b:pres.0000006752.81486.74
83 sgo:license sg:explorer/license/
84 sgo:sdDataset articles
85 rdf:type schema:ScholarlyArticle
86 N03e78326aaf341fbadfa9ba24c4fa0b2 rdf:first sg:person.0672053321.72
87 rdf:rest N7eb0d21fcf07450f86d78069ecd7da27
88 N14d7da2f4e9340d1b63e1d14a8873955 schema:name pubmed_id
89 schema:value 16245051
90 rdf:type schema:PropertyValue
91 N7eb0d21fcf07450f86d78069ecd7da27 rdf:first sg:person.01064603366.33
92 rdf:rest N90d738c224714a3c9d2b649b23e08d96
93 N90d738c224714a3c9d2b649b23e08d96 rdf:first sg:person.01044126157.13
94 rdf:rest Nb84f7fa624894b478ac92c8a3481512e
95 Naae18def8398422aade88e1693cfc552 schema:name Springer Nature - SN SciGraph project
96 rdf:type schema:Organization
97 Nb787d8cf9214456c844f609c863b2114 schema:name dimensions_id
98 schema:value pub.1021746993
99 rdf:type schema:PropertyValue
100 Nb84f7fa624894b478ac92c8a3481512e rdf:first sg:person.0603657647.00
101 rdf:rest rdf:nil
102 Nbed8a73398d448cebe0091f203069041 schema:name doi
103 schema:value 10.1023/b:pres.0000006752.81486.74
104 rdf:type schema:PropertyValue
105 Neee02a0a3f044129a91bf862385c8d62 schema:volumeNumber 78
106 rdf:type schema:PublicationVolume
107 Nfc9a0801b0254d5a8f31f45ccceab1a0 schema:issueNumber 3
108 rdf:type schema:PublicationIssue
109 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
110 schema:name Biological Sciences
111 rdf:type schema:DefinedTerm
112 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
113 schema:name Biochemistry and Cell Biology
114 rdf:type schema:DefinedTerm
115 sg:journal.1022986 schema:issn 0166-8595
116 1573-5079
117 schema:name Photosynthesis Research
118 schema:publisher Springer Nature
119 rdf:type schema:Periodical
120 sg:person.01044126157.13 schema:affiliation grid-institutes:grid.64212.33
121 schema:familyName Goodlett
122 schema:givenName David R.
123 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01044126157.13
124 rdf:type schema:Person
125 sg:person.01064603366.33 schema:affiliation grid-institutes:grid.64212.33
126 schema:familyName Yi
127 schema:givenName Eugene C.
128 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01064603366.33
129 rdf:type schema:Person
130 sg:person.0603657647.00 schema:affiliation grid-institutes:grid.17091.3e
131 schema:familyName Beatty
132 schema:givenName J. Thomas
133 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0603657647.00
134 rdf:type schema:Person
135 sg:person.0672053321.72 schema:affiliation grid-institutes:grid.17091.3e
136 schema:familyName Fejes
137 schema:givenName Anthony P.
138 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0672053321.72
139 rdf:type schema:Person
140 sg:pub.10.1007/0-306-47954-0_12 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031827688
141 https://doi.org/10.1007/0-306-47954-0_12
142 rdf:type schema:CreativeWork
143 sg:pub.10.1007/0-306-47954-0_34 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030117726
144 https://doi.org/10.1007/0-306-47954-0_34
145 rdf:type schema:CreativeWork
146 sg:pub.10.1007/0-306-47954-0_44 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041874390
147 https://doi.org/10.1007/0-306-47954-0_44
148 rdf:type schema:CreativeWork
149 sg:pub.10.1016/1044-0305(94)80016-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018629105
150 https://doi.org/10.1016/1044-0305(94)80016-2
151 rdf:type schema:CreativeWork
152 sg:pub.10.1023/a:1016132700844 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025875146
153 https://doi.org/10.1023/a:1016132700844
154 rdf:type schema:CreativeWork
155 sg:pub.10.1038/10890 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012772847
156 https://doi.org/10.1038/10890
157 rdf:type schema:CreativeWork
158 grid-institutes:grid.17091.3e schema:alternateName Department of Microbiology and Immunology, University of British Columbia, V6T 1Z3, Vancouver, BC, Canada
159 schema:name Department of Microbiology and Immunology, University of British Columbia, V6T 1Z3, Vancouver, BC, Canada
160 rdf:type schema:Organization
161 grid-institutes:grid.64212.33 schema:alternateName The Institute for Systems Biology, 98103, Seattle, WA, USA
162 schema:name The Institute for Systems Biology, 98103, Seattle, WA, USA
163 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...