NEWS

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PSMatch 1.15

PSMatch 1.17.1

• Added parameter z and allCharges in plotSpectraPTM() and labelFragments() and set it to 1:precursorCharge(x) by default when it used to only display charge 1 before. See this PR.

PSMatch 1.17.0

• New Bioconductor devel.

PSMatch 1.15.3

• Adjusted documentation on addCarbamidomethyl = TRUE in calculateFragments() set by default.
• Corrected plotSpectraPTM() relative PTMods dependencies, identifications are highlighted in bold in the USI. Added parameters to call addFixed and addVariable within plotSpectraPTM().
• Add PTMods dependency and thus positional modifications in calculateFragments() (see issue 38)

PSMatch 1.15.2

• Use MsDataHub instead of msdata.

PSMatch 1.15.1

• Fix minor check notes (Rd link and IRanges import)

PSMatch 1.15.0

• New devel version

PSMatch 1.13

PSMatch 1.13.3

• Nothing yet

PSMatch 1.13.2

• Add CITATION to the pre-print (https://doi.org/10.31219/osf.io/62v9p_v2)
• Add possibility to split protein groups in PSM data with makeAdjacencyMatrix (see issue #30)
• Removed showDetails() from setMethod("show", "PSM") as discussed in issue #30
• Add USI parameter to plotSpectraPTM.
• Correct filterPsmFdr output message
• Update Fragments vignette.
• Improve labelFragments()runtime (see issue #25).
• Add Selenocysteine and Pyrrolysine to getAminoAcids().

PSMatch 1.13.1

• Refactor and improve plotSpectraPTM().

PSMatch 1.13.0

• New Bioconductor devel.

PSMatch 1.11

PSMatch 1.11.5

• Correct plotSpectraPTM annotations.

PSMatch 1.11.4

• Added plotSpectraPTM: a plotting function to visualise post-translational modifications.

PSMatch 1.11.3

• Deprecated addFragments. The use of labelFragments is endorsed instead. See PR #20.

PSMatch 1.11.2

• Replace calculateFragments with calculateFragments2. See PR #19.

PSMatch 1.11.1

• New calculateFragments2 function includes fixed and variable modifications to fragments ions. See PR #16.

PSMatch 1.11.0

• New devel version

PSMatch 1.9

PSMatch 1.9.1

• Fix check errors.

PSMatch 1.9.0

• New Bioc devel.

PSMatch 1.7

PSMatch 1.7.2

• Fix connected component dim names in show().

PSMatch 1.7.1

• In addFragments() use ... to pass parameters to calculateFragments().

PSMatch 1.7.0

• New Bioc devel.

PSMatch 1.5

PSMatch 1.5.0

• New Bioc devel.

PSMatch 1.3

PSMatch 1.3.3

• New fdr variable (default is always NA_character_ for now) that defines the spectrum FDR (or any similar/relevant metric that can be used for filtering - see next item).
• New filterPsmFdr() function that filters based on the fdr variable.

PSMatch 1.3.2

• Specific Matrix::rowSums() to fix error in example.

PSMatch 1.3.1

• Fix type in vignette.

PSMatch 1.0

PSMatch 1.0.0

• First Bioconductor release.

PSMatch 0.99

Changes in 0.99.5

• Fix mz calculation in calculateFragments for neutral losses with a charge > 1 (ported from MSnbase - see issue 573).

Changes in 0.99.4

• Set seed in the ConnectedComponents unit test to stop random errors after clustering.

Changes in 0.99.3

• Fix bug in describePeptides() (close #11).

Changes in 0.99.2

• Describe the ConnectedComponents() return value.
• Add/update installation instructions.

Changes in 0.99.1

• Fix typo and improve documentation.

Changes in 0.99.0

• Prepare package for Bioconductor submission.