Changelog

Source: NEWS.md

PTMods 1.1

PTMods 1.1.1

• Added pos parameter in addFixedModifications() to allow positional modifications as they can be defined in some search engine outputs.

PTMods 1.1.0

• New Bioconductor devel.

PTMods 0.99

PTMods 0.99.6

• Adjusted documentation in convertAnnotation().

PTMods 0.99.5

• Import stats::setNames.
• Specify package name when loading data (fixes an https://github.com/lgatto/MSnbase/issues/613).

PTMods 0.99.4

• Added getModificationsCounts()
• convertAnnotation() now also has a verbose parameter to suppress warnings if need be.

PTMods 0.99.3

• Added addModifications(), addFixedModifications(), addVariableModifications(), getCanonicalSequence() and useful PTM utils.

PTMods 0.99.2

• Update PTMods datasets [2026-02-18].
• Improved performance of convertAnnotation() by calling the modifications dataset before .convertAnnotation().

PTMods 0.99.1

• Bump for re-build in Bioconductor submission (due to missing maintainer e-mail address)

PTMods 0.99.0

• Bump version for Bioconductor submission

PTMods 0.3

• Update PTMods datasets [2026-01-02 Fri].
• Rename the package to PTMods and add vignette.
• Add convertAnnotation() to parse and convert between 3 PTM annotation styles. Currently supports unimodId, unimod name and deltaMass.

PTMods 0.2

• Update datasets to latest unimod version.
• In the new unimod version some IDs are duplicated using the current “Name:Site:Position:NeutralLoss” ID scheme. For these we add increasing numbers to the end (“Name:Site:Position:NeutralLoss:DuplicateNumber”).
• Now depends on R 3.5 (serialisation of RData files changed).

PTMods 0.1

• First public version.