A community standard format for the representation of protein affinity reagents

David Erik Immanuel Gloriam; Sandra Orchard; Daniela Bertinetti; Erik Björling; Erik Bongcam-Rudloff; Carl A K Borrebaeck; Julie Bourbeillon; Andrew R M Bradbury; Antoine de Daruvar; Stefan Dübel; Ronald Frank; Toby J Gibson; Larry Gold; Niall Haslam; Friedrich W Herberg; Tara Hiltke; Jörg D Hoheisel; Samuel Kerrien; Manfred Koegl; Zoltán Konthur; Bernhard Korn; Ulf Landegren; Luisa Montecchi-Palazzi; Sandrine Palcy; Henry Rodriguez; Sonja Schweinsberg; Volker Sievert; Oda Stoevesandt; Michael J Taussig; Marius Ueffing; Mathias Uhlén; Silvère van der Maarel; Christer Wingren; Peter Woollard; David J Sherman; Henning Hermjakob

doi:10.1074/mcp.M900185-MCP200

A community standard format for the representation of protein affinity reagents

David Erik Immanuel Gloriam, Sandra Orchard, Daniela Bertinetti, Erik Björling, Erik Bongcam-Rudloff, Carl A K Borrebaeck, Julie Bourbeillon, Andrew R M Bradbury, Antoine de Daruvar, Stefan Dübel, Ronald Frank, Toby J Gibson, Larry Gold, Niall Haslam, Friedrich W Herberg, Tara Hiltke, Jörg D Hoheisel, Samuel Kerrien, Manfred Koegl, Zoltán KonthurBernhard Korn, Ulf Landegren, Luisa Montecchi-Palazzi, Sandrine Palcy, Henry Rodriguez, Sonja Schweinsberg, Volker Sievert, Oda Stoevesandt, Michael J Taussig, Marius Ueffing, Mathias Uhlén, Silvère van der Maarel, Christer Wingren, Peter Woollard, David J Sherman, Henning Hermjakob

31 Citations (Scopus)

Abstract

Protein affinity reagents (PARs), most commonly antibodies, are essential reagents for protein characterization in basic research, biotechnology, and diagnostics as well as the fastest growing class of therapeutics. Large numbers of PARs are available commercially; however, their quality is often uncertain. In addition, currently available PARs cover only a fraction of the human proteome, and their cost is prohibitive for proteome scale applications. This situation has triggered several initiatives involving large scale generation and validation of antibodies, for example the Swedish Human Protein Atlas and the German Antibody Factory. Antibodies targeting specific subproteomes are being pursued by members of Human Proteome Organisation (plasma and liver proteome projects) and the United States National Cancer Institute (cancer-associated antigens). ProteomeBinders, a European consortium, aims to set up a resource of consistently quality-controlled protein-binding reagents for the whole human proteome. An ultimate PAR database resource would allow consumers to visit one on-line warehouse and find all available affinity reagents from different providers together with documentation that facilitates easy comparison of their cost and quality. However, in contrast to, for example, nucleotide databases among which data are synchronized between the major data providers, current PAR producers, quality control centers, and commercial companies all use incompatible formats, hindering data exchange. Here we propose Proteomics Standards Initiative (PSI)-PAR as a global community standard format for the representation and exchange of protein affinity reagent data. The PSI-PAR format is maintained by the Human Proteome Organisation PSI and was developed within the context of ProteomeBinders by building on a mature proteomics standard format, PSI-molecular interaction, which is a widely accepted and established community standard for molecular interaction data. Further information and documentation are available on the PSI-PAR web site.

Original language	English
Journal	Molecular and Cellular Proteomics
Volume	9
Issue number	1
Pages (from-to)	1-10
ISSN	1535-9476
DOIs	https://doi.org/10.1074/mcp.M900185-MCP200
Publication status	Published - Jan 2010

Keywords

Former Faculty of Pharmaceutical Sciences

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1074/mcp.M900185-MCP200

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Gloriam, D. E. I., Orchard, S., Bertinetti, D., Björling, E., Bongcam-Rudloff, E., Borrebaeck, C. A. K., Bourbeillon, J., Bradbury, A. R. M., de Daruvar, A., Dübel, S., Frank, R., Gibson, T. J., Gold, L., Haslam, N., Herberg, F. W., Hiltke, T., Hoheisel, J. D., Kerrien, S., Koegl, M., ... Hermjakob, H. (2010). A community standard format for the representation of protein affinity reagents. Molecular and Cellular Proteomics, 9(1), 1-10. https://doi.org/10.1074/mcp.M900185-MCP200

Gloriam, DEI, Orchard, S, Bertinetti, D, Björling, E, Bongcam-Rudloff, E, Borrebaeck, CAK, Bourbeillon, J, Bradbury, ARM, de Daruvar, A, Dübel, S, Frank, R, Gibson, TJ, Gold, L, Haslam, N, Herberg, FW, Hiltke, T, Hoheisel, JD, Kerrien, S, Koegl, M, Konthur, Z, Korn, B, Landegren, U, Montecchi-Palazzi, L, Palcy, S, Rodriguez, H, Schweinsberg, S, Sievert, V, Stoevesandt, O, Taussig, MJ, Ueffing, M, Uhlén, M, van der Maarel, S, Wingren, C, Woollard, P, Sherman, DJ & Hermjakob, H 2010, 'A community standard format for the representation of protein affinity reagents', Molecular and Cellular Proteomics, vol. 9, no. 1, pp. 1-10. https://doi.org/10.1074/mcp.M900185-MCP200

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title = "A community standard format for the representation of protein affinity reagents",

abstract = "Protein affinity reagents (PARs), most commonly antibodies, are essential reagents for protein characterization in basic research, biotechnology, and diagnostics as well as the fastest growing class of therapeutics. Large numbers of PARs are available commercially; however, their quality is often uncertain. In addition, currently available PARs cover only a fraction of the human proteome, and their cost is prohibitive for proteome scale applications. This situation has triggered several initiatives involving large scale generation and validation of antibodies, for example the Swedish Human Protein Atlas and the German Antibody Factory. Antibodies targeting specific subproteomes are being pursued by members of Human Proteome Organisation (plasma and liver proteome projects) and the United States National Cancer Institute (cancer-associated antigens). ProteomeBinders, a European consortium, aims to set up a resource of consistently quality-controlled protein-binding reagents for the whole human proteome. An ultimate PAR database resource would allow consumers to visit one on-line warehouse and find all available affinity reagents from different providers together with documentation that facilitates easy comparison of their cost and quality. However, in contrast to, for example, nucleotide databases among which data are synchronized between the major data providers, current PAR producers, quality control centers, and commercial companies all use incompatible formats, hindering data exchange. Here we propose Proteomics Standards Initiative (PSI)-PAR as a global community standard format for the representation and exchange of protein affinity reagent data. The PSI-PAR format is maintained by the Human Proteome Organisation PSI and was developed within the context of ProteomeBinders by building on a mature proteomics standard format, PSI-molecular interaction, which is a widely accepted and established community standard for molecular interaction data. Further information and documentation are available on the PSI-PAR web site.",

keywords = "Former Faculty of Pharmaceutical Sciences",

author = "Gloriam, {David Erik Immanuel} and Sandra Orchard and Daniela Bertinetti and Erik Bj{\"o}rling and Erik Bongcam-Rudloff and Borrebaeck, {Carl A K} and Julie Bourbeillon and Bradbury, {Andrew R M} and {de Daruvar}, Antoine and Stefan D{\"u}bel and Ronald Frank and Gibson, {Toby J} and Larry Gold and Niall Haslam and Herberg, {Friedrich W} and Tara Hiltke and Hoheisel, {J{\"o}rg D} and Samuel Kerrien and Manfred Koegl and Zolt{\'a}n Konthur and Bernhard Korn and Ulf Landegren and Luisa Montecchi-Palazzi and Sandrine Palcy and Henry Rodriguez and Sonja Schweinsberg and Volker Sievert and Oda Stoevesandt and Taussig, {Michael J} and Marius Ueffing and Mathias Uhl{\'e}n and {van der Maarel}, Silv{\`e}re and Christer Wingren and Peter Woollard and Sherman, {David J} and Henning Hermjakob",

note = "Keywords: Database Management Systems; Databases, Protein; Humans; International Cooperation; Proteome; Proteomics; Terminology as Topic",

year = "2010",

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doi = "10.1074/mcp.M900185-MCP200",

language = "English",

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T1 - A community standard format for the representation of protein affinity reagents

AU - Gloriam, David Erik Immanuel

AU - Orchard, Sandra

AU - Bertinetti, Daniela

AU - Björling, Erik

AU - Bongcam-Rudloff, Erik

AU - Borrebaeck, Carl A K

AU - Bourbeillon, Julie

AU - Bradbury, Andrew R M

AU - de Daruvar, Antoine

AU - Dübel, Stefan

AU - Frank, Ronald

AU - Gibson, Toby J

AU - Gold, Larry

AU - Haslam, Niall

AU - Herberg, Friedrich W

AU - Hiltke, Tara

AU - Hoheisel, Jörg D

AU - Kerrien, Samuel

AU - Koegl, Manfred

AU - Konthur, Zoltán

AU - Korn, Bernhard

AU - Landegren, Ulf

AU - Montecchi-Palazzi, Luisa

AU - Palcy, Sandrine

AU - Rodriguez, Henry

AU - Schweinsberg, Sonja

AU - Sievert, Volker

AU - Stoevesandt, Oda

AU - Taussig, Michael J

AU - Ueffing, Marius

AU - Uhlén, Mathias

AU - van der Maarel, Silvère

AU - Wingren, Christer

AU - Woollard, Peter

AU - Sherman, David J

AU - Hermjakob, Henning

N1 - Keywords: Database Management Systems; Databases, Protein; Humans; International Cooperation; Proteome; Proteomics; Terminology as Topic

PY - 2010/1

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N2 - Protein affinity reagents (PARs), most commonly antibodies, are essential reagents for protein characterization in basic research, biotechnology, and diagnostics as well as the fastest growing class of therapeutics. Large numbers of PARs are available commercially; however, their quality is often uncertain. In addition, currently available PARs cover only a fraction of the human proteome, and their cost is prohibitive for proteome scale applications. This situation has triggered several initiatives involving large scale generation and validation of antibodies, for example the Swedish Human Protein Atlas and the German Antibody Factory. Antibodies targeting specific subproteomes are being pursued by members of Human Proteome Organisation (plasma and liver proteome projects) and the United States National Cancer Institute (cancer-associated antigens). ProteomeBinders, a European consortium, aims to set up a resource of consistently quality-controlled protein-binding reagents for the whole human proteome. An ultimate PAR database resource would allow consumers to visit one on-line warehouse and find all available affinity reagents from different providers together with documentation that facilitates easy comparison of their cost and quality. However, in contrast to, for example, nucleotide databases among which data are synchronized between the major data providers, current PAR producers, quality control centers, and commercial companies all use incompatible formats, hindering data exchange. Here we propose Proteomics Standards Initiative (PSI)-PAR as a global community standard format for the representation and exchange of protein affinity reagent data. The PSI-PAR format is maintained by the Human Proteome Organisation PSI and was developed within the context of ProteomeBinders by building on a mature proteomics standard format, PSI-molecular interaction, which is a widely accepted and established community standard for molecular interaction data. Further information and documentation are available on the PSI-PAR web site.

AB - Protein affinity reagents (PARs), most commonly antibodies, are essential reagents for protein characterization in basic research, biotechnology, and diagnostics as well as the fastest growing class of therapeutics. Large numbers of PARs are available commercially; however, their quality is often uncertain. In addition, currently available PARs cover only a fraction of the human proteome, and their cost is prohibitive for proteome scale applications. This situation has triggered several initiatives involving large scale generation and validation of antibodies, for example the Swedish Human Protein Atlas and the German Antibody Factory. Antibodies targeting specific subproteomes are being pursued by members of Human Proteome Organisation (plasma and liver proteome projects) and the United States National Cancer Institute (cancer-associated antigens). ProteomeBinders, a European consortium, aims to set up a resource of consistently quality-controlled protein-binding reagents for the whole human proteome. An ultimate PAR database resource would allow consumers to visit one on-line warehouse and find all available affinity reagents from different providers together with documentation that facilitates easy comparison of their cost and quality. However, in contrast to, for example, nucleotide databases among which data are synchronized between the major data providers, current PAR producers, quality control centers, and commercial companies all use incompatible formats, hindering data exchange. Here we propose Proteomics Standards Initiative (PSI)-PAR as a global community standard format for the representation and exchange of protein affinity reagent data. The PSI-PAR format is maintained by the Human Proteome Organisation PSI and was developed within the context of ProteomeBinders by building on a mature proteomics standard format, PSI-molecular interaction, which is a widely accepted and established community standard for molecular interaction data. Further information and documentation are available on the PSI-PAR web site.

KW - Former Faculty of Pharmaceutical Sciences

U2 - 10.1074/mcp.M900185-MCP200

DO - 10.1074/mcp.M900185-MCP200

M3 - Journal article

C2 - 19674966

SN - 1535-9476

VL - 9

SP - 1

EP - 10

JO - Molecular and Cellular Proteomics

JF - Molecular and Cellular Proteomics

IS - 1

ER -

A community standard format for the representation of protein affinity reagents

Abstract

Keywords

UN SDGs

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