While metagenomic and metatranscriptomic approaches share a common technical measurement platform that is fairly uniform and standardized, the experimental protocol for metaproteomics is much more broad and under active development. This presents challenges for assessing and comparing results and capabilities. In addition, metaproteomics currently benefits greatly by the sequencing, assembly, and annotation of metagenomes for accurate interpretation of the data. Thus, to propel metaproteomics to an unprecedented level of microbiome functional analyses requires an expanded and concerted stage of development where all possible synergies between analytical scientists, protein biochemists, bioinformaticians, statisticians, microbiologists, and other multi-omics specialists should be exploited. The current positive momentum of metaproteomics is particularly ripe for such a shift in gear. Importantly, the microbiome research community needs knowledge dissemination via improved educational resources so that community members are informed of the possibilities metaproteomics can offer and have an understanding of the realistic status of the field. Ideally, the microbiome and metaproteomics community should have easier access to the most recent updates of methodologies through specialized open platforms equipped with state-of-the-art instrumentation and strong expertise in data analysis. The full impact of active research to further improve metaproteomics in terms of methodology and data analysis will only be achieved if we improve its standards, educate the whole community, and foster new conceptual advances, thus facilitating the applicability of metaproteomics to solve a wide range of key biological questions. Clearly, metaproteomics has now matured sufficiently to be a viable component of experimental design in current and future microbiome research projects.
A growing community of researchers using metaproteomics had the opportunity to meet at several international symposia (Magdeburg, Germany in February 2016, Alghero, Italy, in June 2017, Leipzig, Germany in December 2018, an online edition in June 2021, and Luxembourg City, Luxembourg in September 2021) and launched specific actions such as training sessions and interlaboratory comparisons. Over the past year, members of this community have regularly discussed a variety of subjects, such as the need for a place where newcomers and experts can discuss and initiate new projects, the desire to forge metaproteomics as a critical methodology of choice for functional analyses, and the need to establish and disseminate the best options and standards for this methodology. This has enabled the development of a roadmap in order to assess the possibilities of tackling more complex projects, such as meta-omics projects and spatio-temporal studies of hundreds of differing conditions involving a large number of samples and replicates to be analyzed at increasing depth and throughput.
This international community, which at the time of writing brings together over 120 members from 48 research groups from 15 countries, has proposed a new initiative under the aegis of the European Proteomics Association (EuPA, https://eupa.org), the federation of European national proteomics societies, with a clear mission and vision statement: “the Metaproteomics Initiative promotes dissemination of metaproteomics fundamentals, advancements, and applications through collaborative networking in microbiome research. We aim to be the central information hub and open meeting place where newcomers and experts interact to communicate, standardize, and accelerate experimental and bioinformatic methodologies in this field”. This will be achieved initially through a dedicated website (https://metaproteomics.org) and Twitter account (@MetaP_Init), presentations and other educational resources, an online communication channel, inter-laboratory comparisons, and regular symposia. We are delighted to announce that as of February 2021 the Metaproteomics Initiative was officially launched and supported by EuPA. We are confident that this Initiative will benefit from an open structure, facilitating exchanges and interactions with other disciplines, and favouring additional synergies at the interfaces with other omics, data science, and microbiology. Through this commentary, we invite the entire microbiome community to join this Initiative and promote collective innovative and holistic approaches to understand how microbiomes function.
The formulation and execution of a community-driven, multi-lab comparison of established metaproteomic workflows, the “Critical Assessment of MetaProteome Investigation” (CAMPI) study, is the first tangible action of the Metaproteomics Initiative [12]. CAMPI has compared sample preparation, mass spectrometry analysis, and bioinformatics workflows for data analysis. This benchmarking effort has led to findings which have highlighted the importance of each step of the analytical pipeline. Such a benchmarking effort calls for discussion not only on the needs of standardized experimental procedures and data treatment workflows, but also specific guidelines in data reporting and data sharing. The CAMPI effort has also paved the way for subsequent inter-laboratory assays where advanced methodological questions will be tackled by the strength and multiple expertises of the whole community. In this regard, it is clear that the definition of appropriate standardized biological samples or benchmark datasets presents important tasks for the community.
Among the other major activities already initiated by the Metaproteomics Initiative are (i) an inaugural online symposium in June 2021, (ii) its promotion among the microbiome community by means of active communication channels, (iii) gathering tutorials and lectures on metaproteomics for offering simple and free access to high-standard educational resources, and (iv) establishment of a consensual framework to stimulate, initiate and coordinate open working groups conducting projects with defined objectives and outputs. To achieve its objectives, the Metaproteomics Initiative will favor the organization of training courses for newcomers and advanced users, further promote its vision in regions currently under-represented, regularly organize new CAMPI editions open to all volunteers, propose brainstorming sessions and hackathons for solving specific bottlenecks, arrange specific round-tables for improving guidelines, and recommending metrics for high-quality results, and establish a platform where scientists with key scientific questions can meet metaproteomics specialists for smooth and efficient collaboration.
As pointed out above, the benefits of a united and stronger metaproteomics community and its successful insertion at the crossroads of many disciplines are huge. Although under the EuPA umbrella, the Metaproteomics Initiative is not limited to a given geographical area and welcomes all positive ideas and feedback. As the puzzling complexity of microbiome samples has been an important driver of methodological improvements in meta-omic sciences, open challenges in metaproteomics are expected to further stimulate significant advancements in mass spectrometry-based proteome analysis and proteome bioinformatics [12, 13]. Due to the myriad of possible applications, metaproteomic approaches are increasingly used and the field is becoming attractive to young scientists. Indeed, a new generation of scientists trained in one or more of the interrelated areas of meta-omics, data science, modeling, and microbiology is emerging. Engaging, inspiring, and educating early-career researchers are undoubtedly a rewarding prospect for the microbiome community.