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tonywu1999 merged 1 commit into from
Apr 23, 2026
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Update NEWS file #199

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10 changes: 10 additions & 0 deletions inst/NEWS.rd
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\title{News for package, \pkg{MSstats}}
\encoding{UTF-8}

\section{Version 4.20.0 (2026-04-23)}{
\itemize{
\item \strong{Protein turnover analysis}: Added support for multi-label summarization, enabling experiments that use multiple isotope labels to quantify protein synthesis and degradation rates. Each isotope label is now summarized independently, giving more accurate per-label abundance estimates.
\item \strong{Protein turnover analysis}: Normalization using unlabeled peptides is now available for protein turnover experiments. Specify \code{nameStandards = "unlabeled"} in \code{dataProcess} to use all unlabeled peptides as references for normalization
\item \strong{Profile plots}: Run-level profile plots in \code{dataProcessPlots} now display 95\% confidence interval bars around summarized protein abundance values when applying anomaly score based feature weighting, giving a direct visual indication of quantification uncertainty across biological replicates.
\item \strong{Global standards normalization}: The reference signal used for normalization is now computed as the median (instead of the mean) across standard peptide measurements, making the normalization more robust to outlier measurements in the reference channel.
\item \strong{Bug fix}: Anomaly-score-based feature weighting could produce invalid weights (division by zero) when all features in a run had identical intensities. A variance floor has also been added to prevent degenerate variance estimates that could distort protein-level summaries.
}
}

\section{Version 4.18.0 (2025-10-15)}{
\itemize{
\item Introduced MSstats+ functionalities.
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