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MSstatsConvert 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.

MSstatsConvert 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.

MSstatsConvert 1.9.1

  • Added DIA-NN converter.

MSstatsConvert 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.

MSstatsConvert 1.2.1

  • Fixed a bug related to SRM inputs.

MSstatsConvert 1.1.2

  • Updated Spectronaut converter to allow annotation in input file.

MSstatsConvert 1.1.1

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

MSstatsConvert 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.

MSstatsConvert 0.0.1

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