The ProteomeXchange consortium at 10 years: 2023 update.

Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) was originally set up to standardize data submission and dissemination of public MS proteomics data. It is now 10 years since the initial data workflow was implemented. In this manuscript, we describe the main developments in PX since the previous update manuscript in Nucleic Acids Research was published in 2020. The six members of the Consortium are PRIDE, PeptideAtlas (including PASSEL), MassIVE, jPOST, iProX and Panorama Public. We report the current data submission statistics, showcasing that the number of datasets submitted to PX resources has continued to increase every year. As of June 2022, more than 34 233 datasets had been submitted to PX resources, and from those, 20 062 (58.6%) just in the last three years. We also report the development of the Universal Spectrum Identifiers and the improvements in capturing the experimental metadata annotations. In parallel, we highlight that data re-use activities of public datasets continue to increase, enabling connections between PX resources and other popular bioinformatics resources, novel research and also new data resources. Finally, we summarise the current state-of-the-art in data management practices for sensitive human (clinical) proteomics data.

The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.

The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) has standardized data submission and dissemination of mass spectrometry proteomics data worldwide since 2012. In this paper, we describe the main developments since the previous update manuscript was published in Nucleic Acids Research in 2017. Since then, in addition to the four PX existing members at the time (PRIDE, PeptideAtlas including the PASSEL resource, MassIVE and jPOST), two new resources have joined PX: iProX (China) and Panorama Public (USA). We first describe the updated submission guidelines, now expanded to include six members. Next, with current data submission statistics, we demonstrate that the proteomics field is now actively embracing public open data policies. At the end of June 2019, more than 14 100 datasets had been submitted to PX resources since 2012, and from those, more than 9 500 in just the last three years. In parallel, an unprecedented increase of data re-use activities in the field, including 'big data' approaches, is enabling novel research and new data resources. At last, we also outline some of our future plans for the coming years.

ProteinExplorer: A Repository-Scale Resource for Exploration of Protein Detection in Public Mass Spectrometry Data Sets.

High-throughput tandem mass spectrometry has enabled the detection and identification of over 75% of all proteins predicted to result in translated gene products in the human genome. In fact, the galloping rate of data acquisition and sharing of mass spectrometry data has led to the current availability of many tens of terabytes of public data in thousands of human data sets. The systematic reanalysis of these public data sets has been used to build a community-scale spectral library of 2.1 million precursors for over 1 million unique sequences from over 19,000 proteins (including spectra of synthetic peptides). However, it has remained challenging to find and inspect spectra of peptides covering functional protein regions or matching novel proteins. ProteinExplorer addresses these challenges with an intuitive interface mapping tens of millions of identifications to functional sites on nearly all human proteins while maintaining provenance for every identification back to the original data set and data file. Additionally, ProteinExplorer facilitates the selection and inspection of HPP-compliant peptides whose spectra can be matched to spectra of synthetic peptides and already includes HPP-compliant evidence for 107 missing (PE2, PE3, and PE4) and 23 dubious (PE5) proteins. Finally, ProteinExplorer allows users to rate spectra and to contribute to a community library of peptides entitled PrEdict (Protein Existance dictionary) mapping to novel proteins but whose preliminary identities have not yet been fully established with community-scale false discovery rates and synthetic peptide spectra. ProteinExplorer can be now be accessed at https://massive.ucsd.edu/ProteoSAFe/protein_explorer_splash.jsp .

A bimodular oxidoreductase mediates the specific reduction of phylloquinone (vitamin K1) in chloroplasts.

Plants and certain species of cyanobacteria are the only organisms capable of synthesizing phylloquinone (vitamin K1 for vertebrates), which they use as an electron carrier during photosynthesis. Recent studies, however, have identified a plastidial pool of non-photoactive phylloquinone that could be involved in additional cellular functions. Here, we characterized an Arabidopsis bimodular enzyme--the At4g35760 gene product--comprising an integral domain homologous to the catalytic subunit of mammalian vitamin K1 epoxide reductase (VKORC1, EC 1.1.4.1) that is fused to a soluble thioredoxin-like moiety. GFP-fusion experiments in tobacco mesophyll cells established that the plant protein is targeted to plastids, and analyses of transcript and protein levels showed that expression is maximal in leaf tissues. The fused and individual VKORC1 domains were separately expressed in yeast, removing their chloroplast targeting pre-sequence and adding a C-terminal consensus signal for retention in the endoplasmic reticulum. The corresponding microsomal preparations were equally effective at mediating the dithiotreitol-dependent reduction of phylloquinone and menaquinone into their respective quinol forms. Strikingly, unlike mammalian VKORC1, the Arabidopsis enzyme did not reduce phylloquinone epoxide, and was resistant to inhibition by warfarin. The isoprenoid benzoquinone conjugates plastoquinone and ubiquinone were not substrates, establishing that the plant enzyme evolved strict specificity for the quinone form of naphthalenoid conjugates. In vitro reconstitution experiments established that the soluble thioredoxin-like domain can function as an electron donor for its integral VKORC1 partner.

Analytical methods for determination of anthraquinone dyes in historical textiles: A review.

Historical and archaeological textiles are among the most crucial and vulnerable records of our social and cultural history. Analysis of organic colorants found in these materials is unquestionably one of the most powerful tools to understand historical developments, cultural exchanges, and progress in science and technology. Natural anthraquinones represent the most commonly used natural colorants for textile dyeing until the late 19th century. The identification of anthraquinones in cultural heritage objects is a challenging task due to the small size of historical samples, diversity of potential dye sources, variable extraction procedures and dyeing methods, complex chemical constitution, structurally analogous chromophores, and possible presence of degradation products and contaminants. Developments in dye analysis of historical interest have originated and expanded along with the general advances in analytical science. In the last few decades, a close cooperation between science and cultural heritage disciplines contributed enormously to this field. The topic of historical dyes and their analysis in textiles, artworks, archaeological objects and cultural heritage materials has been reviewed several times in the last fifteen years. However, no review has been published to-date exclusively on the analysis of anthraquinone colorants in historical and archaeological textiles. Overall, liquid chromatography (LC)-based techniques have been the most widely used method for anthraquinone dye analysis. Owing to increasing demand of minimally invasive/non-invasive techniques, recent developments of novel techniques have resulted in the availability of many alternative/complementary methods to LC-based analysis. This review begins with a short overview of sources, chemistry and importance of natural anthraquinone dyes found in historical textiles before turning to a detailed discussion on developments involving established and emerging analytical techniques of anthraquinone dye analysis for textile cultural heritage materials. To illustrate the state-of-the-art, representative examples of analytical techniques highlighting their advantages, limitations and applicability are also presented.

Characterisation of oil and aluminium complex on replica and historical 19th c. Turkey red textiles by non-destructive diffuse reflectance FTIR spectroscopy.

This work investigates historical and replica Turkey red textiles with diffuse reflectance infrared (DRIFT) spectroscopy to study the coordination complex between cellulose, fatty acids, and the aluminium ions that form the basis of the colour lake. Turkey red was produced in Scotland for around 150 years, and is held in many museum and archive collections. The textile was renowned for its brilliant red hue, and for its fastness to light, washing, rubbing, and bleaching. This was attributed to its unusual preparatory process, the chemistry of which was never fully understood, that involved imbuing cotton with a solution of aqueous fatty acids and then aluminium in the following step. Here we show, for the first time, a characterisation of the Turkey red complex on replica and historical textiles. The development of techniques for non-destructive and in situ analysis of historical textiles is valuable for improving understanding of their chemistry, hopefully contributing to better conservation and display practices. The results show the fatty acids condense onto the cellulose polymer via hydrogen bonding between the CO and OH of the respective compounds, then the aluminium forms a bridging complex with the fatty acid carboxyl. This contributes to an improved understanding of Turkey red textiles, and shows the useful application of handheld diffuse FTIR instruments for heritage textile research.