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Record W2071394295 · doi:10.1074/mcp.t400023-mcp200

A High Throughput Method for the Detection of Metalloproteins on a Microgram Scale

2005· article· en· W2071394295 on OpenAlexaff
Martin Högbom, U.B. Ericsson, Robert Lam, M. Amin Bakali H., Ekaterina Kuznetsova, P. Nordlund, Deborah B. Zamble

Bibliographic record

VenueMolecular & Cellular Proteomics · 2005
Typearticle
Languageen
FieldNursing
TopicTrace Elements in Health
Canadian institutionsUniversity of Toronto
Fundersnot available
KeywordsMetalloproteinChemistryProteomeContext (archaeology)ZincChemiluminescenceMass spectrometryChromatographyBiochemistryEnzymeBiology

Abstract

fetched live from OpenAlex

Proteins that bind transition metals make up a substantial portion of the proteome, and the identification of a metal cofactor in a protein can greatly facilitate its functional assignment and help place it in the context of known cellular pathways. Existing methods for the detection of metalloproteins generally consume large amounts of protein, require expensive equipment, or are very labor intensive, rendering them unsuitable for use in high throughput proteomic initiatives. Here we present a method for the identification of metalloproteins that contain iron, copper, manganese, cobalt, nickel, and/or zinc that is and can is a of and detection it of protein, and of protein metal of protein the the and of the is in a and for a can for metal in a of Proteins that bind transition metals make up a substantial portion of the proteome, and the identification of a metal cofactor in a protein can greatly facilitate its functional assignment and help place it in the context of known cellular pathways. Existing methods for the detection of metalloproteins generally consume large amounts of protein, require expensive equipment, or are very labor intensive, rendering them unsuitable for use in high throughput proteomic initiatives. Here we present a method for the identification of metalloproteins that contain iron, copper, manganese, cobalt, nickel, and/or zinc that is and can is a of and detection it of protein, and of protein metal of protein the the and of the is in a and for a can for metal in a of is the and of and a and of the and of protein, its cellular and and a proteomic of is and the and for high throughput a proteomic in that a very the of proteomic is a and method for high throughput high high identification of transition that metalloproteins make up of the and functional of metal in bind and the identification of a metal cofactor facilitate the functional assignment of a protein and help place it in the context of known cellular in the for for high throughput in of metal can and the protein can the for the of protein or metal of protein it in of of a protein methods for metal of are for or or or consume large amounts of protein or require that can very expensive in large and its for for metalloproteins and in of the of method for transition metal in for that amounts of protein are large of and Here we a method for the detection of that contain the transition metals in iron, copper, manganese, cobalt, nickel, and zinc the of the of the and is that are and detection the known that in the of a and is amounts of the in is a very of transition metals of and the for detection for of and and the of in of the of in and its transition metal in the of a of in the method for in the and is the detection of the metal of the metals a detection for of metal use of in of zinc and of transition is in a in a the method high the of method we protein that is a method for metal and and is the of the of the of protein and the of its high and and the that it can of in is a the methods the and the proteomic and metal the metal the method are the the of and of the of a protein in of the of of a the a a of the of a and the for and for the a the in are the the a a a and in and of metal that of method for transition metal in transition metals a of for of in of transition metals is the that is metals and the in of metal are in a the the of metals the metal of of metal the of of iron, copper, or very manganese, and in the of the and in is the of the the of the of the it the of metals a for copper, manganese, cobalt, nickel, and zinc for the and and of transition we the it is and the metals that are in the the of the of transition metal can for the and a that can the of a of the that the in the for and for and of metal the of the and the of the in of the in and zinc the the metal the in the of the the metal in the metals and zinc can the of for proteomic amounts of are a proteomic consume a of a high of is the of metal of metal the of transition metal and of copper, cobalt, and and of for detection of assignment or for the in is the metal the metals are are a in is a protein of and of the of a in the and the is the in the and a in the is a protein of and of the of zinc the identification of a in and a in the that a of a metal is is a protein of zinc and of the a the zinc in the in the is a protein of and of zinc the is a in the in the and the in the the of or protein is protein of metal and a that of the metals the for or in the of the of metals that can in is the of protein of and zinc in and a the of that is the of the is or a transition metal is the protein metal is can in of the of of the in and metal of the a protein of and of a protein of and of zinc a protein of zinc and of a protein of and of zinc and protein of metal protein protein a metals are are a in a metals are are a in in a of that the metal is and of metal protein, a in the is of protein, the of the and and in the the are of protein is for a and that metalloproteins in contain of we that of protein for the and the is that the of the in the the is a is that the of in the or a is present the are the the of protein the and the the protein and that contain in in and protein a of that are the of protein the detection of transition of of the the the of the and metal of a for of a the copper, manganese, and can in the and copper, nickel, and zinc and can in the or is present in the protein it of a the that metals in for and the of and and the of in of the of in and its of in the method for in the and and are known a of metals are very in and the for and are the present of the protein the the of and of metal or and known metalloproteins protein of the and of protein in in a the method of the or in the in the or the of in the of and in the metal of and the amounts of of the transition metals that a in of the a of iron, of copper, and of zinc in of metal that a and of metal that or the the of the metals in of the the for the and for the are in and that for the of the of the metals that are in a and or that in the of and is and for the is that contain amounts of metal a in and that contain a of metal the or in the the of metal of metal of the and the a or in the are of metal or or or or in a of of metal in the or or or or in a of is the of the the a of protein the of metal the of a protein contain metal that of a we present the in we is the the the of the protein is the are are in the for protein or of the metals and up the is and the the are and for the of is that the metals in the of the for in the of the metal is for of the in the of the of the in the of the metal of metal is and and method for transition metal in of the of methods the of large amounts of protein, the of the and and expensive in large and its for for metalloproteins and in of the of make them unsuitable for proteomic and for in Here we present a method for identification that the of and can method is and in a is for proteomic and is a proteomic copper, manganese, and are in the and nickel, manganese, copper, and are in the for the of metals in it is very it of the use of for the detection of transition is in the methods or and it is that a of can or of are of the of in and its transition metal in the of a and of for of present of the of the is in the that metal in the of and the in the and is for and that the protein the of protein is and in of protein is for the is and the is in the detection of and zinc and the and cobalt, of protein are for is and and the of metal of the metals can for and contain a of identification in the of is metalloproteins of a large of a of the is for of in for is that a in the is the protein, metal and the protein the the method is a the metal of of a known protein that in or that in the proteomic the present method for detection the the protein and and can protein in protein for a high throughput and make it a in the of can for metal in a of a a of that in functional assignment of metal in the in of the method metal identification of the for the of the the is the and of and a and of the and of protein, its cellular and and a proteomic of is and the and for high throughput a proteomic in that a very the of proteomic is a and method for high throughput high high identification of transition that metalloproteins make up of the and functional of metal in bind and the identification of a metal cofactor facilitate the functional assignment of a protein and help place it in the context of known cellular in the for for high throughput in of metal can and the protein can the for the of protein or metal of protein it in of of a protein methods for metal of are for or or or consume large amounts of protein or require that can very expensive in large and its for for metalloproteins and in of the of method for transition metal in for that amounts of protein are large of and Here we a method for the detection of that contain the transition metals in iron, copper, manganese, cobalt, nickel, and zinc the of the of the and is that are and detection the known that in the of a and is amounts of the in is a very of transition metals of and the for detection for of and and the of in of the of in and its transition metal in the of a of in the method for in the and is the detection of the metal of the metals a detection for of metal use of in of zinc and of transition is in a in a the method high the of method we protein that is a method for metal and and is the of the of the of protein and the of its high and and the that it can of in is a the methods the and the proteomic and metal the metal the method are the the of and of the of a protein in of the of of a the a a of the of a and the for and for the a the in are the the a a a and in and of metal that of method for transition metal in and metal the metal the method are the the of and and metal the metal the method are the the of and of the of a protein in of the of of a the a a of the of a and the for and for the a the in are the the a a a and in and of metal that of method for transition metal in of the of a protein in of the of of a the a a of the of a and the for and for the a the in are the the a a a and in and of metal that of method for transition metal in transition metals a of for of in of transition metals is the that is metals and the in of metal are in a the the of metals the metal of of metal the of of iron, copper, or very manganese, and in the of the and in is the of the the of the of the it the of metals a for copper, manganese, cobalt, nickel, and zinc for the and and of transition we the it is and the metals that are in the the of the of transition metal can for the and a that can the of a of the that the in the for and for and the metal the in the of the the metal in the metals and zinc can the of for proteomic amounts of are a proteomic consume a of a high of is the of metal of metal the of transition metal and of copper, cobalt, and and of for detection of assignment or for the in is the metal the metals are are a in is a protein of and of the of a in the and the is the in the and a in the is a protein of and of the of zinc the identification of a in and a in the that a of a metal is is a protein of zinc and of the a the zinc in the in the is a protein of and of zinc the is a in the in the and the in the the of or protein is protein of metal and a that of the metals the for or in the of the of metals that can in is the of protein of and zinc in and a the of that is the of the is or a transition metal is the protein metal is can in of the of of the in and metal of the a protein of and of a protein of and of zinc a protein of zinc and of a protein of and of zinc and protein of metal protein protein a metals are are a in a metals are are a in in a of that the metal is and of metal protein, a in the is of protein, the of the and and in the the are of protein is for a and that metalloproteins in contain of we that of protein for the and the is that the of the in the the is a is that the of in the or a is present the are the the of protein the and the the protein and that contain in in and protein a of that are the of protein the detection of transition of of the the the of the and metal of a for of a the copper, manganese, and can in the and copper, nickel, and zinc and can in the or is present in the protein it of a the that metals in for and the of and and the of in of the of in and its of in the method for in the and and are known a of metals are very in and the for and are the present of the protein the the of and of metal or and known metalloproteins protein of the and of protein in in a the method of the or in the in the or the of in the of and in the metal of and the amounts of of the transition metals that a in of the a of iron, of copper, and of zinc in of metal that a and of metal that or the the of the metals in of the the for the and for the are in and that for the of the of the metals that are in a and or that in the of and is and for the is that contain amounts of metal a in and that contain a of metal the or in the the of metal of metal of the and the a or in the are of metal or or or or in a of of metal in the or or or or in a of is the of the the a of protein the of metal the of a protein contain metal that of a we present the in we is the the the of the protein is the are are in the for protein or of the metals and up the is and the the are and for the of is that the metals in the of the for in the of the metal is for of the in the of the transition metals a of for of in of transition metals is the that is metals and the in of metal are in a the the of metals the metal of of metal the of of iron, copper, or very manganese, and in the of the and in is the of the the of the of the it the of metals a for copper, manganese, cobalt, nickel, and zinc for the and and of transition we the it is and the metals that are in the the of the of transition metal can for the and a that can the of a of the that the in the for and for and the of for proteomic amounts of are a proteomic consume a of a high of is the of metal of metal the of transition metal and of copper, cobalt, and and of for detection transition metals a of for of in of transition metals is the that is metals and the in of metal are in a the the of metals the metal of of metal the of of iron, copper, or very manganese, and in the of the and in is the of the the of the of the it the of metals a for copper, manganese, cobalt, nickel, and zinc for the and and of transition we the it is and the metals that are in the the of the of transition metal can for the and a that can the of a of the that the in the for and for and the of for proteomic amounts of are a proteomic consume a of a high of is the of metal of metal the of transition metal and of copper, cobalt, and and of for detection of assignment or for the in is the metal the metals are are a in is a protein of and of the of a in the and the is the in the and a in the is a protein of and of the of zinc the identification of a in and a in the that a of a metal is is a protein of zinc and of the a the zinc in the in the is a protein of and of zinc the is a in the in the and the in the the of or protein is protein of metal and a that of the metals the for or in the of the of metals that can in is the of protein of and zinc in and a the of that is the of the is or a transition metal is the protein metal is can in protein a metals are are a in a metals are are a in in a of that the metal is and of metal protein, a in the is of protein, the of the and and in the the are of protein is for a and that metalloproteins in contain of we that of protein for the and the is that the of the in the the is a is that the of in the or a is present the are the the of protein the and the the protein and that contain in in and of assignment or for the in is the metal the metals are are a in is a protein of and of the of a in the and the is the in the and a in the is a protein of and of the of zinc the identification of a in and a in the that a of a metal is is a protein of zinc and of the a the zinc in the in the is a protein of and of zinc the is a in the in the and the in the the of or protein is protein of metal and a that of the metals the for or in the of the of metals that can in is the of protein of and zinc in and a the of that is the of the is or a transition metal is the protein metal is can in of that the metal is and of metal protein, a in the is of protein, the of the and and in the the are of protein is for a and that metalloproteins in contain of we that of protein for the and the is that the of the in the the is a is that the of in the or a is present the are the the of protein the and the the protein and that contain in in and protein a of that are the of protein the detection of transition of of the the the of the and metal of a for of a the copper, manganese, and can in the and copper, nickel, and zinc and can in the or is present in the protein it of a the that metals in for and the of and and the of in of the of in and its of in the method for in the and and are known a of metals are very in and the for and are the present protein a of that are the of protein the detection of transition of of the the the of the and metal of a for of a the copper, manganese, and can in the and copper, nickel, and zinc and can in the or is present in the protein it of a the that metals in for and the of and and the of in of the of in and its of in the method for in the and and are known a of metals are very in and the for and are the present of the protein the the of and of metal or and known metalloproteins protein of the and of protein in in a the method of the or in the in the or the of in the of and in the metal of and the amounts of of the transition metals that a in of the a of iron, of copper, and of zinc in of metal that a and of metal that or the the of the metals in of the the for the and for the are in and that for the of the of the metals that are in a and or that in the of and is and for the is that contain amounts of metal a in and that contain a of metal of metal or or or or in a of of metal in the or or or or in a of is the of the the a of protein the of metal the of a protein contain metal that of a we present the in we is the the the of the protein is the are are in the for protein or of the metals and up the is and the the are and for the of is that the metals in the of the for in the of the metal is for of the in the of the protein the the of and of metal or and known metalloproteins protein of the and of protein in in a the method of the or in the in the or the of in the of and in the metal of and the amounts of of the transition metals that a in of the a of iron, of copper, and of zinc in of metal that a and of metal that or the the of the metals in of the the for the and for the are in and that for the of the of the metals that are in a and or that in the of and is and for the is that contain amounts of metal a in and that contain a of metal of is the of the the a of protein the of metal the of a protein contain metal that of a we present the in we is the the the of the protein is the are are in the for protein or of the metals and up the is and the the are and for the of is that the metals in the of the for in the of the metal is for of the in the of the of the in the of the metal of metal is and and method for transition metal in of the of methods the of large amounts of protein, the of the and and expensive in large and its for for metalloproteins and in of the of make them unsuitable for proteomic and for in Here we present a method for identification that the of and can method is and in a is for proteomic and is a proteomic copper, manganese, and are in the and nickel, manganese, copper, and are in the for the of metals in it is very it of the use of for the detection of transition is in the methods or and it is that a of can or of are of the of in and its transition metal in the of a and of for of present of the of the is in the that metal in the of and the in the and is for and that the protein the of protein is and in of protein is for the is and the is in the detection of and zinc and the and cobalt, of protein are for is and and the of metal of the metals can for and contain a of identification in the of is metalloproteins of a large of a of the is for of in for is that a in the is the protein, metal and the protein the the method is a the metal of of a known protein that in or that in the proteomic the present method for detection the the protein and and can protein in protein for a high throughput and make it a in the of can for metal in a of a a of that in functional assignment of metal in the in of the method metal identification of the for the of the the of the in the of the metal of metal is and and method for transition metal in of the of methods the of large amounts of protein, the of the and and expensive in large and its for for metalloproteins and in of the of make them unsuitable for proteomic and for in Here we present a method for identification that the of and can method is and in a is for proteomic and is a proteomic copper, manganese, and are in the and nickel, manganese, copper, and are in the for the of metals in it is very it of the use of for the detection of transition is in the methods or and it is that a of can or of are of the of in and its transition metal in the of a and of for of present of the of the is in the that metal in the of and the in the and is for and that the protein the of protein is and in of protein is for the is and the is in the detection of and zinc and the and cobalt, of protein are for is and and the of metal of the metals can for and contain a of identification in the of is metalloproteins of a large of a of the is for of in for is that a in the is the protein, metal and the protein the the method is a the metal of of a known protein that in or that in the proteomic the present method for detection the the protein and and can protein in protein for a high throughput and make it a in the of can for metal in a of a a of that in functional assignment of metal in the in of the method metal identification of the for the of the the of the protein in and for

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

How this classification was reachedexpand

Full frame distilled prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.

metaresearch head score (Codex)0.001
metaresearch head score (Gemma)0.000
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Bench or experimental · Consensus signal: Bench or experimental
GenreCandidate signal: Methods · Consensus signal: none
Teacher disagreement score0.206
Threshold uncertainty score0.963

Codex and Gemma teacher scores by category

CategoryCodexGemma
Metaresearch0.0010.000
Meta-epidemiology (narrow)0.0000.000
Meta-epidemiology (broad)0.0000.000
Bibliometrics0.0000.000
Science and technology studies0.0000.000
Scholarly communication0.0000.000
Open science0.0000.000
Research integrity0.0000.000
Insufficient payload (model declined to judge)0.0000.000

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.013
GPT teacher head0.292
Teacher spread0.279 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one teacher head, not a consensus.

The models applied no category: nothing in the taxonomy fit this work.
Study designBench or experimental
Domainnot available
GenreMethods

How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".

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Citations36
Published2005
Admission routes1
Has abstractyes

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