The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world’s largest data repository of mass spectrometry-based proteomics data, and is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016. In the last 3 years, public data sharing through PRIDE (as part of PX) has definitely become the norm in the field. In parallel, data re-use of public proteomics data has increased enormously, with multiple applications. We first describe the new architecture of PRIDE Archive, the archival component of PRIDE. PRIDE Archive and the related data submission framework have been further developed to support the increase in submitted data volumes and additional data types. A new scalable and fault tolerant storage backend, Application Programming Interface and web interface have been implemented, as a part of an ongoing process. Additionally, we emphasize the improved support for quantitative proteomics data through the mzTab format. At last, we outline key statistics on the current data contents and volume of downloads, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas.

MaxDIA is a software platform for analyzing data-independent acquisition (DIA) proteomics data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves deep proteome coverage with substantially better coefficients of variation in protein quantification than other software. MaxDIA is equipped with accurate false discovery rate (FDR) estimates on both library-to-DIA match and protein levels, including when using whole-proteome predicted spectral libraries. This is the foundation of discovery DIA—hypothesis-free analysis of DIA samples without library and with reliable FDR control. MaxDIA performs three- or four-dimensional feature detection of fragment data, and scoring of matches is augmented by machine learning on the features of an identification. MaxDIA’s bootstrap DIA workflow performs multiple rounds of matching with increasing quality of recalibration and stringency of matching to the library. Combining MaxDIA with two new technologies—BoxCar acquisition and trapped ion mobility spectrometry—both lead to deep and accurate proteome quantification.

The number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein–protein interactions has increased during the last years. As the technique is now becoming routine for in vitro and in vivo applications in proteomics and structural biology there is a pressing need to define protocols as well as data analysis and reporting formats. Such consensus formats should become accepted in the field and be shown to lead to reproducible results. This first, community-based harmonization study on XL-MS is based on the results of 32 groups participating worldwide. The aim of this paper is to summarize the status quo of XL-MS and to compare and evaluate existing cross-linking strategies. Our study therefore builds the framework for establishing best practice guidelines to conduct cross-linking experiments, perform data analysis, and define reporting formats with the ultimate goal of assisting scientists to generate accurate and reproducible XL-MS results.

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Dilated eye exams are the standard of care to detect advancing, vision threatening, but often asymptomatic retinopathy in a timely fashion, allowing for vision preserving treatments. Annual exam rates are suboptimal, especially in underserved populations. Although teleophthalmology programs tremendously improve annual exam rates in low income/under resourced settings, widespread adoption is limited. Using a mixed methods approach, three focus groups and individual interviews were conducted for patients with type 2 diabetes (N = 23) who had a teleophthalmology exam or a dilated eye exam. A survey and discussion assessed patients' perspectives and value of teleophthalmology, including willingness to pay (WTP). Financial, transportation, and motivational barriers to obtaining an annual dilated eye exam were identified. Patients greatly valued having primary care (PC) based teleophthalmology for its convenience and ability to detect disease to allow for timely treatment and would recommend such a service. Although their WTP was at least the amount of their usual copay, cost was universally cited as a concern. Having a conveniently offered PC based teleophthalmology exam was valued. Educating patients on the value and costs of having such exams may be helpful to encourage informed discussions on eye care, especially in low income, underserved populations. Our study is among the few to provide insight on the value and perceptions of teleophthalmology in US low income, urban minority populations needed to help increase uptake of this innovation. Using surveys followed by facilitated discussion allowed for richer and more varied responses.