Key points are not available for this paper at this time.
Antibodies are useful tools to characterize the components of the human proteome and to validate potential protein biomarkers discovered through various clinical proteomics efforts. The lack of validation results across various applications for most antibodies often makes it necessary to perform cumbersome investigations to ensure specificity of a particular antibody in a certain application. A need therefore exists for a standardized system for sharing validation data about publicly available antibodies and to allow antibody providers as well as users to contribute and edit experimental evidence data, including data also on the antigen. Here we describe a new publicly available portal called Antibodypedia, which has been developed to allow sharing of information regarding validation of antibodies in which providers can submit their own validation results and reliability scores. We report standardized validation criteria and submission rules for applications such as Western blots, protein arrays, immunohistochemistry, and immunofluorescence. The contributor is expected to provide experimental evidence and a validation score for each antibody, and the users can subsequently provide feedback and comments on the use of the antibody. The database thus provides a virtual resource of publicly available antibodies toward human proteins with accompanying experimental evidence supporting an individual validation score for each antibody in an application-specific manner. Antibodies are useful tools to characterize the components of the human proteome and to validate potential protein biomarkers discovered through various clinical proteomics efforts. The lack of validation results across various applications for most antibodies often makes it necessary to perform cumbersome investigations to ensure specificity of a particular antibody in a certain application. A need therefore exists for a standardized system for sharing validation data about publicly available antibodies and to allow antibody providers as well as users to contribute and edit experimental evidence data, including data also on the antigen. Here we describe a new publicly available portal called Antibodypedia, which has been developed to allow sharing of information regarding validation of antibodies in which providers can submit their own validation results and reliability scores. We report standardized validation criteria and submission rules for applications such as Western blots, protein arrays, immunohistochemistry, and immunofluorescence. The contributor is expected to provide experimental evidence and a validation score for each antibody, and the users can subsequently provide feedback and comments on the use of the antibody. The database thus provides a virtual resource of publicly available antibodies toward human proteins with accompanying experimental evidence supporting an individual validation score for each antibody in an application-specific manner. One of the great challenges in basic and clinical proteomics and in bioscience in general is the lack of well characterized affinity reagents for many human protein targets. Such protein-specific probes could be used to explore the corresponding proteins both in vivo and in vitro, including the necessary validation of potential biomarkers discovered through proteomics-based methods such as two-dimensional gels (1Celis J.E. Moreira J.M. Gromova I. Cabezon T. Ralfkiaer U. Guldberg P. Straten P.T. Mouridsen H. Friis E. Holm D. Rank F. Gromov P. Towards discovery-driven translational research in breast cancer.FEBS J. 2005; 272: 2-15Crossref PubMed Scopus (49) Google Scholar) or mass spectrometry (2Tyers M. Mann M. From genomics to proteomics.Nature. 2003; 422: 193-197Crossref PubMed Scopus (770) Google Scholar). An important factor for the use of protein probes is the quality assurance of the affinity reagents regarding specificity and cross-reactivity (3Blow N. Antibodies: the generation game.Nature. 2007; 447: 741-744Crossref PubMed Scopus (38) Google Scholar, 4Uhlén M. Mapping the human proteome using antibodies.Mol. Cell. Proteomics. 2007; 6: 1455-1456Abstract Full Text Full Text PDF PubMed Google Scholar). A recent analysis 1L. Berglund, K. Wester, and M. Uhlén, unpublished data. 1L. Berglund, K. Wester, and M. Uhlén, unpublished data. of more than 5000 antibodies from over 50 commercial providers demonstrated that ∼50% of the antibodies were found to be non-functional in the immunohistochemistry application tested. This demonstrates the need for standardized ways to validate antibodies that is further accentuated by the huge dynamic range of proteins in biological systems as exemplified by the 1010-fold difference in concentration between abundant and low abundance serum proteins in human blood (5Anderson N.L. Anderson N.G. The human plasma proteome: history, character, and diagnostic prospects.Mol. Cell. Proteomics. 2002; 1: 845-867Abstract Full Text Full Text PDF PubMed Scopus (3508) Google Scholar), making potential cross-reactivity difficult to predict, and points to the need to validate affinity reagents in an application-specific manner.Antibodies can be used in many different ways to probe protein function and expression that for many the protein are by various such as or and that by different of the protein by the often are in the it be to use antibodies which are as a of a of to a of the of and of the of PubMed Scopus Google Scholar). such as of or the protein is in a and thus are P. M. of in using protein PubMed Scopus Google Scholar), also in be the of the The of a particular antibody in a is or to predict, and the of an antibody across different application to the a of and to such as specificity and of applications for the most of the proteins for the particular of a protein analysis of using many antibodies by analysis in analysis of protein analysis of of clinical the most of the proteins for the particular in a new An important factor for the generation of affinity reagents is the of M. F. proteomics for human Cell. Proteomics. 2005; Full Text Full Text PDF PubMed Scopus Google Scholar). are different ways to the as in from the of the protein from to of by The most is to use and to the protein or of the protein in is also to the the by the in a called M. is a for an PubMed Scopus Google Scholar). that the of a or of the antibody is by the of used to the affinity as exemplified by the generation of by and protein J. J. M. The of the human PubMed Scopus Google Scholar), the with or proteins often P. M. of in using protein PubMed Scopus Google Scholar). is therefore that most to antibodies in the of proteins or protein research reagents for Western or often are using or protein M. E. E. P. K. H. D. M. J. M. K. I. M. M. K. M. J. J. K. E. P. J. P. I. E. J. J. M. J. M. F. M. H. E. J. H. J. K. U. F. A human protein for and on antibody Cell. Proteomics. 2005; Full Text Full Text PDF PubMed Scopus Google Scholar). The that the the of the affinity reagents across different demonstrates the to publicly the or the as of the for a particular of protein or from protein using different protein protein by protein by low to affinity in a new has been that an for proteomics M. Mapping the human proteome using antibodies.Mol. Cell. Proteomics. 2007; 6: 1455-1456Abstract Full Text Full Text PDF PubMed Google Scholar) be to antibodies and of the protein to the quality of the specificity also to allow various of Anderson N.L. H. J. M. A resource to proteins and of for the a Cell. Proteomics. Full Text Full Text PDF PubMed Scopus Google Scholar). This for a database by the to allow of information about information with a antibody as an important in the of affinity reagents for a particular M. N.G. H. M. E. J.E. F. D. E. K. J. J. D. P. K. J.M. F. Gromov P. F. F. P. K. H. K. N. P. P. K. I. U. M. M. P. F. Mann M. J. M. J. H. H. M. M. K. P. J. J. T. K. K. M. M. M. J. J. J.M. M. T. J. M. P. sharing of human protein PubMed Scopus Google Scholar) the which is an to and proteomics data in a the contributor is expected to provide experimental evidence for the data and with the that the contributor can edit the data. the of proteomics data, of the data to be and the of the portal is to and by to of and experimental information M. N.G. H. M. E. J.E. F. D. E. K. J. J. D. P. K. J.M. F. Gromov P. F. F. P. K. H. K. N. P. P. K. I. U. M. M. P. F. Mann M. J. M. J. H. H. M. M. K. P. J. J. T. K. K. M. M. M. J. J. J.M. M. T. J. M. P. sharing of human protein PubMed Scopus Google Scholar). The need to be to information about and application-specific validation of affinity reagents the need for a database portal for antibodies on we describe an information database that has been developed the of the research D. J. D. H. M. E. U. J. M. P. M. M. M. a resource of affinity reagents for analysis of the human 2007; PubMed Scopus Google Scholar) to a virtual resource of antibodies available to the The portal users to validation results on antibodies and and we report the of applications and the rules for submission of we for the a portal to validation data for publicly available antibodies with accompanying data about the antigen. This new portal thus provides a submission to allow antibody to submit data about their antibodies with validation for various is to submit antibodies available to the and the portal provides to allow users to the corresponding antibody the validation information to the The database on validation by the antibody on a of validation it is important to that the validation is in is thus to submit the data, in the of an with to allow users to the data the validation are also to in comments to the portal about the use of a particular antibody, and in both and results from a particular antibody can be the The of the data in the portal is we that that the standardized and the submission rules been and that the validation score is by evidence validation score is application-specific with the that antibodies can in different The results can also on the used and the of the A of the and the therefore be as of the validation as exemplified in can be to the for each application a of validation be and we that subsequently be the validation and The for sharing antibody data to in a to has been for protein data M. J. P. J. M. M. J. J. P. M. P. N. M. M. J. I. D. H. The information for a 2007; PubMed Scopus Google is important to that the validation of antibodies regarding specificity is and on the concentration and dynamic range of the protein as well as the concentration of A antibody with cross-reactivity to human protein the abundance and thus the concentration of the protein is as with the The specificity of an is thus on the of the protein as with human is also that most of the are and or across the the with is the to antibody and to for huge in dynamic range between different protein targets. is also to validate a particular antibody with a antibody to a of the protein it is important that the antibodies which could to the cross-reactivity an important of the is to the submission of data about the to ensure that antibodies the on the protein it is to perform more of antibodies and to submit such information to the portal to more information in the a particular is or are many different of affinity that can be used as protein probes to explore the human proteome M. as a in PubMed Scopus Google Scholar). research antibodies are by the most used affinity including antibodies by of antibody of PubMed Scopus Google Scholar) or antibodies in which the antibody is using P. of for 2003; PubMed Scopus Google Scholar) or protein P. K. J. M. J. E. H. K. F. M. Towards a human proteome generation of antibodies for 2005; PubMed Scopus Google Scholar). the of new methods M. as a in PubMed Scopus Google Scholar) it in the to affinity reagents in a using in of the portal therefore allow the also of affinity including new protein proteins from PubMed Scopus Google Scholar), such as and and affinity such as also be to also information about to protein such as or low of portal information about antibodies the of the M. E. E. P. K. H. D. M. J. M. K. I. M. M. K. M. J. J. K. E. P. J. P. I. E. J. J. M. J. M. F. M. H. E. J. H. J. K. U. F. A human protein for and on antibody Cell. Proteomics. 2005; Full Text Full Text PDF PubMed Scopus Google Scholar), in the antibody providers are to submit their own antibodies to the virtual The portal thus antibodies in which submission has been by the antibody This is in to the which antibodies by a analysis of immunohistochemistry using a standardized of human and E. P. J. M. F. A for in on protein in and Cell. Proteomics. Full Text Full Text PDF PubMed Scopus Google Scholar). The protein thus provides expression of human proteins in and on the portal antibody by of the applications in the portal and of or in the protein we a new virtual resource for antibodies that has been in an application-specific manner. validation criteria are for research more applications can be in The of the portal is to allow antibody providers to submit validation results for their antibodies and to users of antibodies to antibodies in a particular The is to a resource of antibodies to human proteins to the experimental of the human proteome and to the analysis of potential biomarkers discovered through various clinical proteomics efforts. One of the great challenges in basic and clinical proteomics and in bioscience in general is the lack of well characterized affinity reagents for many human protein targets. Such protein-specific probes could be used to explore the corresponding proteins both in vivo and in vitro, including the necessary validation of potential biomarkers discovered through proteomics-based methods such as two-dimensional gels (1Celis J.E. Moreira J.M. Gromova I. Cabezon T. Ralfkiaer U. Guldberg P. Straten P.T. Mouridsen H. Friis E. Holm D. Rank F. Gromov P. Towards discovery-driven translational research in breast cancer.FEBS J. 2005; 272: 2-15Crossref PubMed Scopus (49) Google Scholar) or mass spectrometry (2Tyers M. Mann M. From genomics to proteomics.Nature. 2003; 422: 193-197Crossref PubMed Scopus (770) Google Scholar). An important factor for the use of protein probes is the quality assurance of the affinity reagents regarding specificity and cross-reactivity (3Blow N. Antibodies: the generation game.Nature. 2007; 447: 741-744Crossref PubMed Scopus (38) Google Scholar, 4Uhlén M. Mapping the human proteome using antibodies.Mol. Cell. Proteomics. 2007; 6: 1455-1456Abstract Full Text Full Text PDF PubMed Google Scholar). A recent analysis 1L. Berglund, K. Wester, and M. Uhlén, unpublished data. 1L. Berglund, K. Wester, and M. Uhlén, unpublished data. of more than 5000 antibodies from over 50 commercial providers demonstrated that ∼50% of the antibodies were found to be non-functional in the immunohistochemistry application tested. This demonstrates the need for standardized ways to validate antibodies that is further accentuated by the huge dynamic range of proteins in biological systems as exemplified by the 1010-fold difference in concentration between abundant and low abundance serum proteins in human blood (5Anderson N.L. Anderson N.G. The human plasma proteome: history, character, and diagnostic prospects.Mol. Cell. Proteomics. 2002; 1: 845-867Abstract Full Text Full Text PDF PubMed Scopus (3508) Google Scholar), making potential cross-reactivity difficult to predict, and points to the need to validate affinity reagents in an application-specific manner. Antibodies can be used in many different ways to probe protein function and expression that for many the protein are by various such as or and that by different of the protein by the often are in the it be to use antibodies which are as a of a of to a of the of and of the of PubMed Scopus Google Scholar). such as of or the protein is in a and thus are P. M. of in using protein PubMed Scopus Google Scholar), also in be the of the The of a particular antibody in a is or to predict, and the of an antibody across different application to the a of and to such as specificity and An important factor for the generation of affinity reagents is the of M. F. proteomics for human Cell. Proteomics. 2005; Full Text Full Text PDF PubMed Scopus Google Scholar). are different ways to the as in from the of the protein from to of by The most is to use and to the protein or of the protein in is also to the the by the in a called M. is a for an PubMed Scopus Google Scholar). that the of a or of the antibody is by the of used to the affinity as exemplified by the generation of by and protein J. J. M. The of the human PubMed Scopus Google Scholar), the with or proteins often P. M. of in using protein PubMed Scopus Google Scholar). is therefore that most to antibodies in the of proteins or protein research reagents for Western or often are using or protein M. E. E. P. K. H. D. M. J. M. K. I. M. M. K. M. J. J. K. E. P. J. P. I. E. J. J. M. J. M. F. M. H. E. J. H. J. K. U. F. A human protein for and on antibody Cell. Proteomics. 2005; Full Text Full Text PDF PubMed Scopus Google Scholar). The that the the of the affinity reagents across different demonstrates the to publicly the or the as of the for a particular antibody. has been that an for proteomics M. Mapping the human proteome using antibodies.Mol. Cell. Proteomics. 2007; 6: 1455-1456Abstract Full Text Full Text PDF PubMed Google Scholar) be to antibodies and of the protein to the quality of the specificity also to allow various of Anderson N.L. H. J. M. A resource to proteins and of for the a Cell. Proteomics. Full Text Full Text PDF PubMed Scopus Google Scholar). This for a database by the to allow of information about information with a antibody as an important in the of affinity reagents for a particular M. N.G. H. M. E. J.E. F. D. E. K. J. J. D. P. K. J.M. F. Gromov P. F. F. P. K. H. K. N. P. P. K. I. U. M. M. P. F. Mann M. J. M. J. H. H. M. M. K. P. J. J. T. K. K. M. M. M. J. J. J.M. M. T. J. M. P. sharing of human protein PubMed Scopus Google Scholar) the which is an to and proteomics data in a the contributor is expected to provide experimental evidence for the data and with the that the contributor can edit the data. the of proteomics data, of the data to be and the of the portal is to and by to of and experimental information M. N.G. H. M. E. J.E. F. D. E. K. J. J. D. P. K. J.M. F. Gromov P. F. F. P. K. H. K. N. P. P. K. I. U. M. M. P. F. Mann M. J. M. J. H. H. M. M. K. P. J. J. T. K. K. M. M. M. J. J. J.M. M. T. J. M. P. sharing of human protein PubMed Scopus Google Scholar). The need to be to information about and application-specific validation of affinity reagents the need for a database portal for antibodies on Here we describe an information database that has been developed the of the research D. J. D. H. M. E. U. J. M. P. M. M. M. a resource of affinity reagents for analysis of the human 2007; PubMed Scopus Google Scholar) to a virtual resource of antibodies available to the The portal users to validation results on antibodies and and we report the of applications and the rules for submission of data. we for the a portal to validation data for publicly available antibodies with accompanying data about the antigen. This new portal thus provides a submission to allow antibody to submit data about their antibodies with validation for various is to submit antibodies available to the and the portal provides to allow users to the corresponding antibody the validation information to the The database on validation by the antibody on a of validation it is important to that the validation is in is thus to submit the data, in the of an with to allow users to the data the validation are also to in comments to the portal about the use of a particular antibody, and in both and results from a particular antibody can be the The of the data in the portal is we that that the standardized and the submission rules been and that the validation score is by evidence validation score is application-specific with the that antibodies can in different The results can also on the used and the of the A of the and the therefore be as of the validation as exemplified in can be to the for each application a of validation be and we that subsequently be the validation and The for sharing antibody data to in a to has been for protein data M. J. P. J. M. M. J. J. P. M. P. N. M. M. J. I. D. H. The information for a 2007; PubMed Scopus Google is important to that the validation of antibodies regarding specificity is and on the concentration and dynamic range of the protein as well as the concentration of A antibody with cross-reactivity to human protein the abundance and thus the concentration of the protein is as with the The specificity of an is thus on the of the protein as with human is also that most of the are and or across the the with is the to antibody and to for huge in dynamic range between different protein targets. is also to validate a particular antibody with a antibody to a of the protein it is important that the antibodies which could to the cross-reactivity an important of the is to the submission of data about the to ensure that antibodies the on the protein it is to perform more of antibodies and to submit such information to the portal to more information in the a particular is or are many different of affinity that can be used as protein probes to explore the human proteome M. as a in PubMed Scopus Google Scholar). research antibodies are by the most used affinity including antibodies by of antibody of PubMed Scopus Google Scholar) or antibodies in which the antibody is using P. of for 2003; PubMed Scopus Google Scholar) or protein P. K. J. M. J. E. H. K. F. M. Towards a human proteome generation of antibodies for 2005; PubMed Scopus Google Scholar). the of new methods M. as a in PubMed Scopus Google Scholar) it in the to affinity reagents in a using in of the portal therefore allow the also of affinity including new protein proteins from PubMed Scopus Google Scholar), such as and and affinity such as also be to also information about to protein such as or low of portal information about antibodies the of the M. E. E. P. K. H. D. M. J. M. K. I. M. M. K. M. J. J. K. E. P. J. P. I. E. J. J. M. J. M. F. M. H. E. J. H. J. K. U. F. A human protein for and on antibody Cell. Proteomics. 2005; Full Text Full Text PDF PubMed Scopus Google Scholar), in the antibody providers are to submit their own antibodies to the virtual The portal thus antibodies in which submission has been by the antibody This is in to the which antibodies by a analysis of immunohistochemistry using a standardized of human and E. P. J. M. F. A for in on protein in and Cell. Proteomics. Full Text Full Text PDF PubMed Scopus Google Scholar). The protein thus provides expression of human proteins in and on the portal antibody by of the applications in the portal and of or in the protein we a new virtual resource for antibodies that has been in an application-specific manner. validation criteria are for research more applications can be in The of the portal is to allow antibody providers to submit validation results for their antibodies and to users of antibodies to antibodies in a particular The is to a resource of antibodies to human proteins to the experimental of the human proteome and to the analysis of potential biomarkers discovered through various clinical proteomics efforts. Here we for the a portal to validation data for publicly available antibodies with accompanying data about the antigen. This new portal thus provides a submission to allow antibody to submit data about their antibodies with validation for various is to submit antibodies available to the and the portal provides to allow users to the corresponding antibody the validation information to the The database on validation by the antibody on a of validation it is important to that the validation is in is thus to submit the data, in the of an with to allow users to the data the validation are also to in comments to the portal about the use of a particular antibody, and in both and results from a particular antibody can be the The of the data in the portal is we that that the standardized and the submission rules been and that the validation score is by evidence data. The validation score is application-specific with the that antibodies can in different The results can also on the used and the of the A of the and the therefore be as of the validation as exemplified in can be to the for each application a of validation be and we that subsequently be the validation and The for sharing antibody data to in a to has been for protein data M. J. P. J. M. M. J. J. P. M. P. N. M. M. J. I. D. H. The information for a 2007; PubMed Scopus Google Scholar). is important to that the validation of antibodies regarding specificity is and on the concentration and dynamic range of the protein as well as the concentration of A antibody with cross-reactivity to human protein the abundance and thus the concentration of the protein is as with the The specificity of an is thus on the of the protein as with human is also that most of the are and or across the the with is the to antibody and to for huge in dynamic range between different protein targets. is also to validate a particular antibody with a antibody to a of the protein it is important that the antibodies which could to the cross-reactivity an important of the is to the submission of data about the to ensure that antibodies the on the protein it is to perform more of antibodies and to submit such information to the portal to more information in the a particular is or are many different of affinity that can be used as protein probes to explore the human proteome M. as a in PubMed Scopus Google Scholar). research antibodies are by the most used affinity including antibodies by of antibody of PubMed Scopus Google Scholar) or antibodies in which the antibody is using P. of for 2003; PubMed Scopus Google Scholar) or protein P. K. J. M. J. E. H. K. F. M. Towards a human proteome generation of antibodies for 2005; PubMed Scopus Google Scholar). the of new methods M. as a in PubMed Scopus Google Scholar) it in the to affinity reagents in a using in of the portal therefore allow the also of affinity including new protein proteins from PubMed Scopus Google Scholar), such as and and affinity such as also be to also information about to protein such as or low The of portal information about antibodies the of the M. E. E. P. K. H. D. M. J. M. K. I. M. M. K. M. J. J. K. E. P. J. P. I. E. J. J. M. J. M. F. M. H. E. J. H. J. K. U. F. A human protein for and on antibody Cell. Proteomics. 2005; Full Text Full Text PDF PubMed Scopus Google Scholar), in the antibody providers are to submit their own antibodies to the virtual The portal thus antibodies in which submission has been by the antibody This is in to the which antibodies by a analysis of immunohistochemistry using a standardized of human and E. P. J. M. F. A for in on protein in and Cell. Proteomics. Full Text Full Text PDF PubMed Scopus Google Scholar). The protein thus provides expression of human proteins in and on the portal antibody by of the applications in the portal and of or in the protein we a new virtual resource for antibodies that has been in an application-specific manner. validation criteria are for research more applications can be in The of the portal is to allow antibody providers to submit validation results for their antibodies and to users of antibodies to antibodies in a particular The is to a resource of antibodies to human proteins to the experimental of the human proteome and to the analysis of potential biomarkers discovered through various clinical proteomics efforts. We are to and for with with
Björling et al. (Wed,) studied this question.