Cloudy with a Chance of Peptides: Accessibility, Scalability, and Reproducibility with Cloud-Hosted Environments

• Published in: Journal of proteome research 2021-04, Vol.20 (4), p.2076-2082
• Main Author: Neely, Benjamin A
• Format: Article
• Language: English
• Subjects: Animals; Computational Biology; Peptides; Proteomics; Reproducibility of Results; Software
• ISSN: 1535-3893; 1535-3907
• DOI: 10.1021/acs.jproteome.0c00920

Cloud-hosted environments offer known benefits when computational needs outstrip affordable local workstations, enabling high-performance computation without a physical cluster. What has been less apparent, especially to novice users, is the transformative potential for cloud-hosted environments to bridge the digital divide that exists between poorly funded and well-resourced laboratories, and to empower modern research groups with remote personnel and trainees. Using cloud-based proteomic bioinformatic pipelines is not predicated on analyzing thousands of files, but instead can be used to improve accessibility during remote work, extreme weather, or working with under-resourced remote trainees. The general benefits of cloud-hosted environments also allow for scalability and encourage reproducibility. Since one possible hurdle to adoption is awareness, this paper is written with the nonexpert in mind. The benefits and possibilities of using a cloud-hosted environment are emphasized by describing how to setup an example workflow to analyze a previously published label-free data-dependent acquisition mass spectrometry data set of mammalian urine. Cost and time of analysis are compared using different computational tiers, and important practical considerations are described. Overall, cloud-hosted environments offer the potential to solve large computational problems, but more importantly can enable and accelerate research in smaller research groups with inadequate infrastructure and suboptimal local computational resources.