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We formulate a general approach to the inclusion of theoretical uncertainties, specifically those related to the missing higher order uncertainty (MHOU), in the determination of parton distribution functions (PDFs). We demonstrate how, under quite generic assumptions, theory uncertainties can be included as an extra contribution to the covariance matrix when determining PDFs from data. We then review, clarify, and systematize the use of renormalization and factorization scale variations as a means to estimate MHOUs consistently in deep inelastic and hadronic processes. We define a set of prescriptions for constructing a theory covariance matrix using scale variations, which can be used in global fits of data from a wide range of different processes, based on choosing a set of independent scale variations suitably correlated within and across processes. We set up an algebraic framework for the choice and validation of an optimal prescription by comparing the estimate of MHOU encoded in the next-to-leading order (NLO) theory covariance matrix to the observed shifts between NLO and NNLO predictions. We perform a NLO PDF determination which includes the MHOU, assess the impact of the inclusion of MHOUs on the PDF central values and uncertainties, and validate the results by comparison to the known shift between NLO and NNLO PDFs. We finally study the impact of the inclusion of MHOUs in a global PDF determination on LHC cross-sections, and provide guidelines for their use in precision phenomenology. In addition, we also compare the results based on the theory covariance matrix formalism to those obtained by performing PDF determinations based on different scale choices.

The parton distribution functions (PDFs) which characterize the structure of the proton are currently one of the dominant sources of uncertainty in the predictions for most processes measured at the Large Hadron Collider (LHC). Here we present the first extraction of the proton PDFs that accounts for the missing higher order uncertainty (MHOU) in the fixed-order QCD calculations used in PDF determinations. We demonstrate that the MHOU can be included as a contribution to the covariance matrix used for the PDF fit, and then introduce prescriptions for the computation of this covariance matrix using scale variations. We validate our results at next-to-leading order (NLO) by comparison to the known next order (NNLO) corrections. We then construct variants of the NNPDF3.1 NLO PDF set that include the effect of the MHOU, and assess their impact on the central values and uncertainties of the resulting PDFs., 8 pages, 6 figures, PDF sets available from https://data.nnpdf.science/nnpdf31_th/. Final Version, to be published in EPJC letters. Appendix removed, several small improvements including brief discussion of usage