Blind spots on western blots: a meta-research study highlighting opportunities to improve figures and methods reporting

Abstract

Western blotting is a standard laboratory method used to detect proteins and assess their expression levels. Unfortunately, poor western blot image display practices and a lack of detailed methods reporting can limit a reader’s ability to evaluate or reproduce western blot results. While several groups have studied the prevalence of image manipulation or provided recommendations for improving western blotting, data on the prevalence of common publication practices are scarce. We systematically examined 551 articles published in the top 25% of journals in neurosciences (n=151) and cell biology (n=400) that contained western blot images, focusing on practices that may omit important information. Our data show that most published western blots are cropped and blot source data are not made available to readers in the supplement. Publishing blots with visible molecular weight markers is rare, and many blots additionally lack molecular weight labels. Western blot methods sections often lack information on the amount of protein loaded on the gel, blocking steps and antibody labeling protocol. Important antibody identifiers like source, catalog number or RRID were omitted frequently for primary antibodies, and regularly for secondary antibodies. We present detailed descriptions and visual examples to help scientists, peer reviewers and editors to publish more informative western blot figures and methods. Additional resources include a toolbox to help scientists produce more reproducible western blot data, teaching slides in English and Spanish and an antibody reporting template.

Blind spots on western blots: Assessment of common problems in western blot figures and methods reporting with recommendations to improve them

“…All full-length original research articles that contained at least 1 image of a western blot were included in the analysis ( S2 Fig ). Subsequently, information from each publication was abstracted by 2 independent reviewers (see: Materials and methods section, supplementary materials and supporting information deposited in our OSF repository at https://osf.io/2c4wq/ [ 24 ]).…”

“…Labels that annotate <1% are not shown. The data underlying this figure can be found at https://osf.io/2c4wq/ [24]. https://doi.org/10.1371/journal.pbio.3001783.g003…”

“…One question related to reporting of replicates was eliminated from both protocols during data abstraction ( Box 1 ). The full protocols are available in the OSF repository at https://osf.io/2c4wq [ 24 ].…”

“…Data visualization for Figs 3 and 4 were created using Python-based Jupyter Notebooks (RRID:SCR_018315, version 6.3.0). Code is available in our repository [ 24 ]. Each panel of Fig 3 was compiled separately and combined with the vector graphic software Adobe Illustrator (RRID:SCR_010279, version 26.0.3).…”

“…Data visualization for Figs 3 and 4 were created using Python-based Jupyter Notebooks (RRID:SCR_018315, version 6.3.0). Code is available in our repository [24]. Each panel of…”