The challenges with the validation of research antibodies

Voskuil, Jan

doi:10.12688/f1000research.10851.1

Cited by 55 publications

(43 citation statements)

References 26 publications

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“…Even though there is a high demand for better antibody characterization, it is not economically attractive to perform the characterization for all the existing items [29], and furthermore to characterize the batch-to-batch variability. Moreover, the characterization only describes the performance of the antibody in the tested application method and thus it is not guaranteed to have the same binding efficiency in other set-ups.…”

Section: Discussionmentioning

confidence: 99%

“…Recently, several studies have pointed out the quality issues and traceability problem concerning commercial antibodies and the lack of quality in the antibody market has been widely recognized by the scientific community [19][20][21][22][23][24][25][26][27][28]. Often, the characterization and specifications provided by the manufacturers are somewhat incomplete and, furthermore, the authors often fail to identify the exact antibody used [28][29][30] for other researchers to be able to purchase the same product. Here, we reviewed published studies using commercial anti-histamine antibodies (excluding IHC and ICC applications).…”

Section: Commercial Anti-histamine Antibodies and Their Use In Immunomentioning

confidence: 99%

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Challenges in Developing a Biochip for Intact Histamine Using Commercial Antibodies

2017

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This study describes the development and the challenges in the development of an on-chip immunoassay for histamine using commercially available antibodies. Histamine can be used as an indicator of food freshness and quality, but it is also a relevant marker in clinical diagnostics. Due to its low molecular weight, simple structure and thus low immunogenicity production of high specificity and affinity antibodies is difficult. From six commercial anti-histamine antibodies tested, only two bound the histamine free in the solution. A fluorescent on-chip immunoassay for histamine was established with a dynamic range of 8-111 µg/mL using polyclonal anti-histamine antibody H7403 from Sigma (Mendota Heights, MN, USA). The anti-histamine antibodies described and used in published literature are thoroughly reviewed and the quality of commercial antibodies and their traceability and quality issues are highlighted and extensively discussed.

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Section: Discussionmentioning

confidence: 99%

Section: Commercial Anti-histamine Antibodies and Their Use In Immunomentioning

confidence: 99%

Challenges in Developing a Biochip for Intact Histamine Using Commercial Antibodies

2017

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“…26 As one of the most prevalent tools in modern-day biological research, they represent an easy target raising the ire of disgruntled scientists as they are known in many cases to display a high level of variability between sources. 27 These issues with antibodies, however, cannot be discovered in most papers because in most papers, even today, these reagents are not cited in a way that makes it easy to even understand which antibody has been used. Antibodies have long been one of least identified resources ( Fig 1C).…”

Section: Analysis Of Reporting Trendsmentioning

confidence: 99%

Rigor and Transparency Index, a new metric of quality for assessing biological and medical science methods

Menke¹,

Roelandse²,

Özyurt

et al. 2020

Preprint

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The reproducibility crisis in science is a multifaceted problem involving practices and incentives, both in the laboratory and in publication. Fortunately, some of the root causes are known and can be addressed by scientists and authors alike. After careful consideration of the available literature, the National Institutes of Health identified several key problems with the way that scientists conduct and report their research and introduced guidelines to improve the rigor and reproducibility of pre-clinical studies. Many journals have implemented policies addressing these same criteria. We currently have, however, no comprehensive data on how these guidelines are impacting the reporting of research. Using SciScore, an automated tool developed to review the methods sections of manuscripts for the presence of criteria associated with the NIH and other reporting guidelines, e.g., ARRIVE, RRIDs, we have analyzed ~1.6 million PubMed Central papers to determine the degree to which articles were addressing these criteria. The tool scores each paper on a ten point scale identifying sentences that are associated with compliance with criteria associated with increased rigor (5 pts) and those associated with key resource identification and authentication (5 pts). From these data, we have built the Rigor and Transparency Index, which is the average score for analyzed papers in a particular journal. Our analyses show that the average score over all journals has increased since 1997, but remains below five, indicating that less than half of the rigor and reproducibility criteria are routinely addressed by authors. To analyze the data further, we examined the prevalence of individual criteria across the literature, e.g., the reporting of a subject's sex (21-37% of studies between 1997 and 2019), the inclusion of sample size calculations (2-10%), whether the study addressed blinding (3-9%), or the identifiability of key biological resources such as antibodies (11-43%), transgenic organisms (14-22%), and cell lines (33-39%). The greatest increase in prevalence for rigor criteria was seen in the use of randomization of subjects (10-30%), while software tool identifiability improved the most among key resource types (42-87%). We further analyzed individual journals over time that had implemented specific author guidelines covering rigor criteria, and found that in some journals, they had a big impact, whereas in others they did not. We speculate that unless they are enforced, author guidelines alone do little to improve the number of criteria addressed by authors. Our Rigor and Transparency Index did not correlate with the impact factors of journals.

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“…Given recent studies concerning high variability in antibody production, LCMS-based methods are an attractive alternative approach for the rapid identification of small molecules, proteins, and peptides in clinical settings where consistency is paramount. 9,10 In the 15 years since the 2003 SARS outbreak, LCMS technology has experienced a revolution led primarily by increases in the speed, sensitivity, and resolution of MS instruments. Today, protein array and antibody-based methods are falling out of favor in both research and clinical diagnostics, due in large part to the improvements in LCMS technology.…”

Section: Introductionmentioning

confidence: 99%

In silicoapproach toward the identification of unique peptides from viral protein infection: Application to COVID-19

Orsburn

Jenkins

Miller

et al. 2020

Preprint

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The novel coronavirus disease first identified in 2019 in Wuhan, has become a serious global public health concern. One current issue is the ability to adequately screen for the virus causing COVID-2 (SARS-CoV-2). Here we demonstrate the feasibility of shotgun proteomics as a SARS-CoV-2 screening method, through the detection of viral peptides in proteolytically digested body fluids. Using in silico methods, we generated trypsin-based shotgun proteomics methods optimized for LCMS systems from 5 commercial instrument vendors (Thermo, SCIEX, Waters, Shimadzu, and Agilent). First, we generated protein FASTA files and their protein digest maps. Second, the FASTA files were used to generate spectral libraries based on experimental data. Third, transition lists were derived from the

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The challenges with the validation of research antibodies

Cited by 55 publications

References 26 publications

Challenges in Developing a Biochip for Intact Histamine Using Commercial Antibodies

Challenges in Developing a Biochip for Intact Histamine Using Commercial Antibodies

Rigor and Transparency Index, a new metric of quality for assessing biological and medical science methods

In silicoapproach toward the identification of unique peptides from viral protein infection: Application to COVID-19

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