The May Editorial in Nature Methods discusses how the overall efficiency of research can be improved by comparative analysis of research method and tool performance.
Although such analysis studies aren’t considered as ‘sexy’ as basic exploratory research, the benefits for and gratitude from the community can be profound. Large well-funded laboratories are more likely to have the resources to perform such analyses and should not discount the advantages to performing such studies and publishing the results.
Nature Methods has published several such analysis studies in the past. A (probably incomplete) selection is listed below. We will strive to publish even more in the future. Our ‘Analysis’ article type is actually dedicated to these kinds of studies. We encourage communities and labs to both contribute such analyses and suggest methodological areas that would benefit from them. The selection below may provide some inspiration.
Multiple-laboratory comparison of microarray platforms
Independence and reproducibility across microarry platforms
Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations
A guide to choosing fluorescent proteins
Reproducible isolation of distinct, overlapping segments of the phosphoproteome
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
Cost-effective strategies for completing the interactome
Cyclic nucleotide analogs as probes of signaling pathways
A HUPO test sample study reveals common problems in mass spectrometry-based proteomics
Comprehensive comparative analysis of strand-specific RNA sequencing methods
Microbial community resemblance methods differ in their ability to detect biologically relevant patterns
Validation of two ribosomal RNA removal methods for microbial metatranscriptomics
Chemically defined conditions for human iPSC derivation and culture
Two-photon absorption properties of fluorescent proteins