NEWS

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msPurity 1.30.1

• Update example for purityX causing build error

msPurity 1.27.1

• createMSP fix - now uses the median precursor MZ and precursor RT in the MSP file

msPurity 1.21.2

• Fixes due to mz and intensity being named in columns for mzR and XCMS
• Fixes for connection{base} file() opening changes (no longer accept w+a in function in R v4.2)
• Update tests for the above
• Update a reference of grpid in averageXFragSpectra functions more explicit (no change in functionality)
• Typo fix in vignette

msPurity 1.21.1

• Bugfix for frag4feature for XCMS 3 compatability https://github.com/computational-metabolomics/msPurity/pull/93
• Remove imports that are no longer used

msPurity 1.19.2

• XCMS 3 compatability update (M-R-JONES) https://github.com/computational-metabolomics/msPurity/pull/91

msPurity 1.19.1

• Bug fix for flagRemove (full width was not calculated as expected)

msPurity 1.17.2

• Update dev to match bug fixes in master

msPurity 1.17.1

• Update dev to match bug fixes in master

msPurity 1.16.2

• Author list updated

msPurity 1.16.1

• Update of createDatabase to record all intra average spectra in database
• Add license and copyright info to code
• Add github workflow CI (and subsequent formatting updates to pass tests)

msPurity 1.15.1

• Update dev to match bug fixes in master

msPurity 1.14.1

• Update of rdpc algorithm (see https://github.com/computational-metabolomics/msPurity/issues/78)
• Update of align algorithm (see https://github.com/computational-metabolomics/msPurity/issues/79)
• Fix for spectralMatching of type 'scan' previously incorrectly outputing no matches

msPurity 1.13.2

• Update dev to match bug fixes in master

msPurity 1.13.1

• Update dev to match bug fixes in master

msPurity 1.13.0

• Bioconductor dev (automatic version bump)

msPurity 1.12.2

• Fix to allow large files to be processed with combineAnnotation (in some cases the summary report should be excluded)

msPurity 1.12.1

• Bug fix for combineAnnotations - MS1 lookup not handling CAMERA adducts correctly
• Fillpeaks bug fix see github #68
• Documentation fixes

msPurity 1.12.0

• Bioconductor release (automatic version bump)

msPurity 1.11.5

• frag4feature fileid fix for conversion from factor to character
• Add missing plyr:: reference (thanks jsaintvanne)

msPurity 1.11.3

• Overhaul of combineAnnotation function. Uses local database now as previously API calls would take too much time to finish and was not usable
• Various updates of createMSP to make compatible with Galaxy workflows
• Parameter added to purityA to allow user to change the PPM tolerance for MZ values between scans when calculated the interpolated precursor ion purity
• Update of spectralMatching results columns to include additional details (e.g. retention time)
• Update of spectralMatching so that either PostgreSQL or MySQL database can be used as input to either query or library

msPurity 1.11.2

• Bug fix for EIC with MSMS data

msPurity 1.11.1

• Bug fix for duplicate MSP spectra when not using metadata table
• Added xcms3 to xcmsSet conversion for "create database" code
• Fix for sirius combine annotations (incorrect column format)

msPurity 1.11.0

• Bioconductor dev (automatic version bump)

msPurity 1.10.0

• Bioconductor release (automatic version bump)

msPurity 1.9.12

• Troublshoot mac "[MSData::Spectrum::getMZIntensityPairs()] Sizes do not match" error

msPurity 1.9.11

• Bug fix for createMSP - now handles metadata with duplicate grpids

msPurity 1.9.10

• Documentation updates

msPurity 1.9.9

• NEW FUNCTION: createDatabase o Updated version of create_database that uses an updated schema
• NEW FUNCTION: spectralMatching o Updated version spectral_matching that allows for more flexibility
• Vignettes and documentation update

msPurity 1.9.8

• NEW FUNCTION: filterFragSpectra (for purityA objects) o LC-MS/MS filtering of spectra (prior to averaging)
• NEW FUNCTIONS: averageIntraFragSpectra, averageInterFragSpectra, averageAllFragSpectra (for purityA objects) o LC-MS/MS averaging and filtering functionality
• NEW FUNCTION: createMSP o Create msp files from purityA objects where XCMS features have been linked to fragmentation spectra
• Updated create_database and spectral matching to have the option to use averaged fragmentation spectra

msPurity 1.9.2

• Bug fix for groupPeaks and groupPeaksEx (the ppm argument was not working and there was inconsistent behaviour with larger datasets). Thanks to Elliot for spotting (https://github.com/litepalmer)
• Updated documentation for spectral matching

msPurity 1.7.6

• create_sql bug fix for msms spectra table. Was crashing due to incorrect ordering.
• Add peak processing (flag remove peaks) for LC-MS XCMS data
• Add option to for frag4feature to just link to the grouped peak rtmin and rtmax (e.g. do not need to link to individual files)

msPurity 1.6.1

• Bug fix. For pos/neg switching acquisition two files are can be generated when converting from RAW to mzML (1 for pos, 1 for neg). The resulting files retention time scans were not being tracked properly in msPurity in these cases. This is now fixed. Thanks to Julien (https://github.com/jsaintvanne) for spotting the bug.

msPurity 1.5.1

• Updates for database creation (can use CAMERA objects now)
• averageSpectra parameter 'MSFileReader' deprecated MSFileReader. Should use csvFile instead, MSFileReader option will still work but a warning will be given

msPurity 1.4.1

• Updates for Galaxy for Spectral Matching
• Spectral matching ra_thres_t bugfix
• Separation of sqlite database creation. Now can be called on it's own or with frag4feature (allows the Galaxy tool to be simplified)

msPurity 1.3.9

• Added very basic SIMS stitch compatibility
• pcalc can handle NAs
• Update of purityX to handle obiwarp RT correction (requires recording the RT RAW at an earlier step)
• bug fix for when library spectra is bigger than target spectra (thanks Martin)

msPurity 1.3.1

• Add spectral matching functionality for LC-MS/MS

msPurity 1.1.1

• Added pcalc functions to be used by user
• Added option to remove isotopes from calculation

msPurity 0.99.10

• Troubleshooting windows build failure

msPurity 0.99.9

• Offset bug fixed (previous only using extracting lower offset from mzML file)
• Updated handling of RT corrected xcmsSet objects for frag4feature function
• Additional column added for tracking ms/ms spectra

msPurity 0.99.8

• User option to change the mzR backend library

msPurity 0.99.4

• Troubleshooting mac build failure

msPurity 0.99.3

• Grouping multiple peaklist into one wide dataframe
• Peaklists can now be averaged across each class using the function groupPeaks() for the class purityD
• A list of dataframes can also be grouped together using the function groupPeakEx()

msPurity 0.99.2

• Updated class names purityPD to purityD
• Updated class names purityLC to purityX
• Updated vignette to reflect slightly different terminology
• Added normalised TIC option for purityD msPurity v0.99.0 (Release date: 2016-04-08)
• Initial release!