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Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments.

ABSTRACT: Analyzing proteins from single cells by tandem mass spectrometry (MS) has recently become technically feasible. While such analysis has the potential to accurately quantify thousands of proteins across thousands of single cells, the accuracy and reproducibility of the results may be undermined by numerous factors affecting experimental design, sample preparation, data acquisition and data analysis. We expect that broadly accepted community guidelines and standardized metrics will enhance rigor, data quality and alignment between laboratories. Here we propose best practices, quality controls and data-reporting recommendations to assist in the broad adoption of reliable quantitative workflows for single-cell proteomics. Resources and discussion forums are available at https://single-cell.net/guidelines .

SUBMITTER: Gatto L

PROVIDER: S-EPMC10130941 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature

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Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments.

Gatto Laurent L Aebersold Ruedi R Cox Juergen J Demichev Vadim V Derks Jason J Emmott Edward E Franks Alexander M AM Ivanov Alexander R AR Kelly Ryan T RT Khoury Luke L Leduc Andrew A MacCoss Michael J MJ Nemes Peter P Perlman David H DH Petelski Aleksandra A AA Rose Christopher M CM Schoof Erwin M EM Van Eyk Jennifer J Vanderaa Christophe C Yates John R JR Slavov Nikolai N

Nature methods 20230302 3

Analyzing proteins from single cells by tandem mass spectrometry (MS) has recently become technically feasible. While such analysis has the potential to accurately quantify thousands of proteins across thousands of single cells, the accuracy and reproducibility of the results may be undermined by numerous factors affecting experimental design, sample preparation, data acquisition and data analysis. We expect that broadly accepted community guidelines and standardized metrics will enhance rigor, ...[more]

PMID: 36864200

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Project description:BackgroundIn the data pipeline from the data collection process to the planned statistical analyses, initial data analysis (IDA) typically takes place between the end of the data collection and do not touch the research questions. A systematic process for IDA and clear reporting of the findings would help to understand the potential shortcomings of a dataset, such as missing values, or subgroups with small sample sizes, or shortcomings in the collection process, and to evaluate the impact of these shortcomings on the research results. A clear reporting of findings is also relevant when making datasets available to other researchers. Initial data analyses can provide valuable insights into the suitability of a data set for a future research study. Our aim was to describe the practice of reporting of initial data analyses in observational studies in five highly ranked medical journals with focus on data cleaning, screening, and reporting of findings which led to a potential change in the analysis plan.MethodsThis review was carried out using systematic search strategies with eligibility criteria for articles to be reviewed. A total of 25 papers about observational studies were selected from five medical journals published in 2018. Each paper was reviewed by two reviewers and IDA statements were further discussed by all authors. The consensus was reported.ResultsIDA statements were reported in the methods, results, discussion, and supplement of papers. Ten out of 25 papers (40%) included a statement about data cleaning. Data screening statements were included in all articles, and 18 (72%) indicated the methods used to describe them. Item missingness was reported in 11 papers (44%), unit missingness in 15 papers (60%). Eleven papers (44%) mentioned some changes in the analysis plan. Reported changes referred to missing data treatment, unexpected values, population heterogeneity and aspects related to variable distributions or data properties.ConclusionReporting of initial data analyses were sparse, and statements on IDA were located throughout the research articles. There is a lack of systematic reporting of IDA. We conclude the article with recommendations on how to overcome shortcomings in the practice of IDA reporting in observational studies.

Dataset Information

Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments.

Publications

Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments.

Similar Datasets

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