Exploring the potential of public proteomics data

Abstract

In a global effort for scientific transparency, it has become feasible and good practice to share experimental data supporting novel findings. Consequently, the amount of publicly available MS‐based proteomics data has grown substantially in recent years. With some notable exceptions, this extensive material has however largely been left untouched. The time has now come for the proteomics community to utilize this potential gold mine for new discoveries, and uncover its untapped potential. In this review, we provide a brief history of the sharing of proteomics data, showing ways in which publicly available proteomics data are already being (re‐)used, and outline potential future opportunities based on four different usage types: use, reuse, reprocess, and repurpose. We thus aim to assist the proteomics community in stepping up to the challenge, and to make the most of the rapidly increasing amount of public proteomics data.

A Golden Age for Working with Public Proteomics Data

“…In the proteomics field, too, there have been several examples of widely debated, controversial findings [21]. These healthy discussions were triggered and enabled naturally by the public availability of the corresponding data sets.…”

CSF-PR 2.0: An Interactive Literature Guide to Quantitative Cerebrospinal Fluid Mass Spectrometry Data from Neurodegenerative Disorders

“…In some cases, it was also difficult to link the values presented in the paper to the data provided in the corresponding supplementary files. In order to enable the comparison of data from different studies it is therefore vital that results are accessible and easily extractable, and that sufficient information is provided to be able to categorize the studies correctly (48,49).…”

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“…For example, it can be used to reprocess raw data in more coherent way, or with novel research questions in mind [177]. Proteomics This article is protected by copyright.…”