Quality standards in proteomics research facilities

Science & Society19 May 2021Open Access Quality standards in proteomics research facilities Common and quality procedures are essential for their users Cristina Chiva orcid.org/0000-0001-8150-6203 Centre de Regulació Genòmica, Barcelona Institute of Technology (BIST), Barcelona, Spain Univeristat Pompeu Fabra, Search more papers by this author Teresa Mendes Maia orcid.org/0000-0003-0038-9629 VIB Proteomics Core, VIB, Ghent, Belgium VIB-UGent Center Medical Biotechnology, Department Biomolecular Medicine, Ghent University, Christian Panse orcid.org/0000-0003-1975-3064 Functional Genomics Zurich, University/ETH Switzerland Swiss Bioinformatics, Lausanne, Karel Stejskal orcid.org/0000-0001-7835-8123 Research Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria IMBA Biotechnology the Austrian Academy Sciences, Thibaut Douché orcid.org/0000-0001-8627-6726 Institut Pasteur, Platform, Mass Spectrometry Biology Unit, USR CNRS 2000 MSBio CNRS, Paris, France Mariette Matondo Damarys Loew orcid.org/0000-0002-9111-8842 Curie, Recherche, Laboratoire Spectrométrie Masse Protéomique, PSL Paris cedex 05, Dominic Helm Core Facility, European Laboratory, Heidelberg, Germany MS based Protein analysis Facilities, DKFZ, Mandy Rettel orcid.org/0000-0002-8304-3385 Karl Mechtler orcid.org/0000-0002-3392-9946 Gregor Mendel (GMI), BioCenter 7 Francis Impens orcid.org/0000-0003-2886-9616 Paolo Nanni Corresponding Author [email protected] orcid.org/0000-0001-8429-3557 Anna Shevchenko Max Planck Cell Genetics, Dresden, Eduard Sabidó orcid.org/0000-0001-6506-7714 Information Chiva1,2, Maia3,4,5, Panse6,7, Stejskal8,9, Douché10, Matondo10, Loew11, Helm12,13, Rettel12, Mechtler8,9,14, Impens3,4,5, *,6, *,15 *,1,2 1Centre 2Univeristat 3VIB 4VIB-UGent 5Department 6Functional 7Swiss 8Research 9IMBA 10Institut 11Institut 12Proteomics 13MS 14Gregor 15Max *Corresponding author. E-mail: EMBO Reports (2021)22:e52626https://doi.org/10.15252/embr.202152626 PDFDownload PDF article text main figures. ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions Figures Info infrastructures have become an part scientific ecosystem. In field proteomics, national international networks platforms been established during past decade that supposed set high-quality services, promote exchange professional information, enable access cutting-edge, specialized technologies. Either centralized or distributed, these technology generating massive amounts data community, support a broad range translational, computational multi-omics initiatives basic projects. By delegating work researchers expect core facility adjusts analytical protocols appropriately project acquire conforming best practice community. The implementation assessment measures commonly accepted controls generation is therefore crucially important scientists who rely on them. However, current control motley collection protocols, standards, reference compounds software tools. relies customized multi-step workflow typically consisting sample preparation, acquisition processing, each step differs among facilities. For example, preparation involves enzymatic digestion proteins, which can be performed in-solution, in-gel, on-beads, with often different proteolytic enzymes, chemicals, conditions laboratories. Data particular instrument up, acquired spectra chromatograms processed tools provided equipment vendors, third parties developed in-house. …current Moreover, implement own guidelines monitor performance entire workflow, utilizing commercially available such as pre-digested cell lysates, recombinant protein mixtures, isotopically labeled peptides. Currently, there no clear consensus if, when how perform checks. There even less walk-in facilities, where staff only responsible correct usage instruments select execute themselves. It not surprising stability robustness applied approach unclear, compromises rigor. Establishing standardized practices Initiated HUPO Standard Initiative (PSI) than ago, MIAPE (Minimal about Experiment; Taylor et al, 2007) introduced common formats sharing reporting data, including unrestricted raw at public repositories (Vizcaíno 2014). Supported journals’ request deposition into condition publication, grown rich resource mining integration. did imply metrics still generic tool capable independently ascertaining technical deposited data. importance assessments open-access was highlighted Amsterdam Principles 10 years ago (Rodriguez 2009), but development threshold delegated central repositories. A few later, Sydney workshop convened US National Cancer made recommendations formulated key principles metrics, journal editors reviewers were encourage enforce (Kinsinger 2012). corollary recognized “the need formal comparison methods equal footing” thus alluding first time control. More recently, indeed included publishing (Abbatiello 2017). has also emphasized associations. Association Facilities (ABRF), Technologies Life Sciences (CTLS), (C4L), Clinical Proteomic Tumor Analysis Consortium (CPTAC), initiated discussions procedures, continuously practices. recent comprehensive survey across Europe showed majority do recognize (Kos-Braun 2020). we believe issue systematic received attention it deserves. maintain community efforts toward sufficiently organized achieve agreement, despite availability evaluation intra- inter-laboratory reproducibility, automated monitoring performance. controls. ensure quality, comparability, integrity. representative example benefit coordinated several units dissection validation SARS interaction map (Gordon foster reuse resources, protect against bias experimental design improve daily routines (Fig 1). Systematic performance, early recognition poor-quality carry-over background signals long-term reproducibility leverage impact aging turnaround laboratory staff. Figure 1. Benefits Main benefits customers, Download figure PowerPoint should flexible diverse workflows instrumental platforms. hubs operations not, limited routine measurements. Diversity model organisms, scales, goals generate numerous project-specific great variability workflows. Instrumentation will remain heterogeneous foreseeable future. choice mass spectrometry defined requirements influenced funding results generations, types, vendors within same facility. framework accommodates Such peptide that—alone spiked samples—are systematically analyzed values relevant control, number identified retention intensity chromatographic peaks, ratio, fold change endogenous These repeated test runs would document individual batch. information highly valuable detecting random failures, stability, ensuring analyses, continuous optimization developing new methods. parameters submitted along result required guidelines. … frequent standard samples help laboratory-based average references drift indicate whether settings optimal readjustment. records could diagnose malfunction instruments. future, integrated both streamline management values. aforementioned towards ISO (International Organization Standardization) other certifications require it. role funders providers schemes pose challenge from agencies. must define parameters, controlled vocabulary, file collective testing anonymized results. They checks vendors’ software. Last least, bodies raise awareness procedure order secure financial support. position drive extensive collaboration concerted efforts. Within alliance (Meder 2016; Lippens 2019) (https://coreforlife.eu), our laboratories advocate policies high services. Among initiatives, endorsed QCloud cross-platform open-source (Chiva 2018; Olivella 2021). further automated, user-friendly, suitable satisfy protection affordable broader practical understanding funding, bodies. Acknowledgements CRG/UPF Unit Spanish Infrastructure Omics (ICTS OmicsTech) member ProteoRed PRB3 consortium supported grant PT17/0019 PE I + D+i 2013-2016 Instituto Salud Carlos III (ISCIII) ERDF. We acknowledge Ministry Science, Innovation Universities, “Centro Excelencia Severo Ochoa 2013-2017”, SEV-2012- 0208, “Secretaria d’Universitats i Recerca del Departament d’Economia Coneixement la Generalitat Catalunya” (2017SGR595). acknowledges Tech Watch Fund FWO-SBO Project S006617N. lab ERA-CAPS 3686 Fund. Union's Horizon 2020 innovation program under agreement No 823839 (EPIC-XS). thankful Andrej fruitful critical reading manuscript rest setting up right environment stimulating ideas. References Abbatiello S, Ackermann BL, Borchers C, Bradshaw RA, Carr SA, Chalkley R, Choi M, Deutsch E, Domon B, Hoofnagle AN al (2017) New publication manuscripts describing application targeted measurements peptides proteins. 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Nat Biotechnol 25: 887–893CrossrefCASPubMedWeb Vizcaíno JA, Wang Csordas Reisinger F, Ríos Dianes Sun Z, Farrah T, Bandeira N (2014) ProteomeXchange provides globally submission dissemination. 32: 223–226CrossrefCASPubMedWeb Previous ArticleNext Article Read MoreAbout coverClose modalView large imageVolume 22,Issue 6,04 June 2021This month's cover highlights PI3KC2? inactivation stabilizes VE?cadherin junctions preserves vascular integrity Typhaine Anquetil, Marie?Pierre Gratacap colleagues showing genetic inhibition reduces cerebral infarction ischemia/reperfusion mouse stroke model. shows coronal brain sections wild?type (left) knock?in mice (right) following ischemic stroke. TTC staining used detect infarcted area pink (pseudocolor). (Scientific image Anquetil Gratacap, Cardiovascular Metabolic Diseases (I2MC), Inserm UMR?1048, Toulouse, France.) Volume 22Issue 64 2021In FiguresReferencesRelatedDetailsLoading ...