Changes in version 1.22.0                        

Protein Turnover Support

  - DIA-NN: DIANNtoMSstatsFormat now accepts a labeledAminoAcids
    parameter to enable protein turnover workflows. Provide the
    single-letter amino acid codes that carry the SILAC label (e.g.
    c("K") or c("K", "R")). The converter automatically distinguishes
    heavy and light peptide forms — either from a Channel column in
    DIA-NN 2.x exports, or by parsing SILAC modification tags (e.g.
    (SILAC-K-H)) in DIA-NN 1.x exports — and populates the
    IsotopeLabelType column required by MSstats downstream.

  - Spectronaut: SpectronauttoMSstatsFormat now accepts a heavyLabels
    parameter to classify peptides in protein turnover experiments.
    Supply the label names as they appear in square brackets in the
    peptide sequence (e.g. c("Lys6") or c("Lys6", "Arg10")). Peptides
    are automatically assigned as heavy (H), light (L), or unlabeled.
    Any novel label name reported by Spectronaut (e.g. "Leu6", "Phe10")
    is supported.

  - Spectronaut: A new peptideSequenceColumn parameter lets you specify
    which column in your Spectronaut export contains the peptide
    sequence. This is especially useful for protein turnover reports,
    which may use a different column layout than a standard Spectronaut
    output.

  - Spectronaut: Protein turnover reports that lack fragment-level
    columns (e.g. FFrgLossType, FFrgIon) are now handled automatically —
    previously these required manual pre-processing before import.

  - Fraction selection: The algorithm that selects the best fraction for
    each peptide feature now correctly accounts for heavy and light
    isotope channels in protein turnover data, ensuring that
    light-channel coverage is prioritized when choosing fractions. When
    multiple fractions have identical coverage, the fraction with the
    highest mean intensity is chosen.

DIA-NN Quality Control: Anomaly Detection

  - DIANNtoMSstatsFormat now supports automated data quality scoring via
    an isolation-forest anomaly detection model (calculateAnomalyScores
    = TRUE). When enabled, each precursor-level feature receives an
    anomaly score that can be used downstream in MSstats to down-weight
    measurements that look like outliers. Users supply the quality
    metric columns to use as model features (anomalyModelFeatures) and,
    optionally, a run order table (runOrder) to engineer temporal trend
    features that detect gradual instrument drift across an experiment.

Spectronaut: MS1 Quantification

  - SpectronauttoMSstatsFormat now accepts "FG.MS1Quantity" (and other
    raw Spectronaut column names) as the intensity argument, in addition
    to the existing "PeakArea" and "NormalizedPeakArea" options.

                       Changes in version 1.16.0                        

  - Improved memory management for efficiency.
  - Added support for ProteinProspector data conversion to MSstatsTMT
    format.
  - Updated NA handling for Skyline and Spectronaut converters
  - Added MetaMorpheus converter functionality.

                        Changes in version 1.9.1                        

  - Added DIA-NN converter.

                        Changes in version 1.5.1                        

  - Fixed bugs related to data types.
  - Fixed bug that resulted in missing TechReplicate column in output.
  - Added Philosopher converter.
  - Added methods for MSstatsValidated objects.

                        Changes in version 1.2.1                        

  - Fixed a bug related to SRM inputs.

                        Changes in version 1.1.2                        

  - Updated Spectronaut converter to allow annotation in input file.

                        Changes in version 1.1.1                        

  - Minor bug fixes
  - Updated MSstatsLogsSettings function to allow differents settings
    for different packages

                       Changes in version 0.99.0                        

  - Added logging utitilies: MSstatsLogsSettings, MSstatsSaveSesionInfo.
  - Added functions for importing and cleaning data: MSstatsImport,
    MSstatsClean.
  - Added functions for preprocessing: MSstatsMakeAnnotation,
    MSstatsPreprocess, MSstatsBalancedDesign.
  - Added vignette.

                        Changes in version 0.0.1                        

  - Added a NEWS.md file to track changes to the package.