Changes in version 1.3.3 - Removed unused dependency. Changes in version 1.3.2 - Reporthing the fixed Modifications if the mqpar.xml is present. Changes in version 1.3.1 - Added median to the PlotAndromedaScore(). - Remove warnings from the vignettes. - Now MQmetrics can read the mqpar.xml file. This one must be located on the same directory as the combined folder. - Reporting the number of threads used by MaxQuant if found the mqpar.xml file. Changes in version 1.1.8 - Fixed test that was resulting in error duet to version 1.1.6 updated way to read the files. Changes in version 1.1.7 - Removed parentheses from the news that was causing issues in Bioconductor. Changes in version 1.1.6 - Bug fixed: If a table was missing, the report was not generated. Changes in version 1.1.5 - The plot generated by PlotPTM() will now indicate (in the legend title) whether the Post-Translational modifications have been aggregated or not as a result of the parameter aggregate_PTMs. - The function PlotPeptidesIdentified() and PlotProteinsIdentified() now return a plot containing Missing Values, Frequency of Identified by Match Between Runs and Frequency of identified by MS/MS. With this, the funciton PlotIdentificationType() becomes obsolete. - The function PlotProteinCoverage() now can take as input multiple UniprotID in a vector format. - The function PlotPTMAcrossSamples() now can take as input multiple PTM_of_Interest in a vector format. - Change in the function make_MQCombined() to read faster the tables and reducing the overall time required to generate a report. Changes in version 1.1.4 - The function PlotProteinCoverage() now reports the coverage individually in each plot rather than the total protein coverage. - MQmetrics now is adapted to MaxQuant v.2.x, since the column names are different than in MaxQuant v.1.x. MQmetrics will detect the MaxQuant version used and read the columns accordingly. - Enhanced error message in PlotiRT() and PlotiRTScore() when irt peptides are note found. Enhanced error message for PlotProteinCoverage() when the UniprotID is not found. Changes in version 1.1.3 - Added new function PlotPTMAcrossSamples(), it takes as input one PTM of interest and shows its intensities across the samples. This function is similar to PlotPTM() but in more detail. - In the function PlotPTM() a parameter combine_same_residue_ptms has been added. It combines multiple PTMs happening in the same residue such as: Dimethyl (KR), Trimethyl (KR). Changes in version 1.1.2 - Fixed units of time MaxQuantAnalysisInfo() when experiment lasting longer than a day. - Added new line to MaxQuantAnalyssInfo() showing when the experiment ended. - Improved aesthethics in the plots from PlotCombinedDynamicRange() and PlotAllDynamicRange(). Changes in version 1.1.1 - Added pagination to PlotiRT() and PlotiRTScore(). - Updated vignette style to Bioconductor's. - Improved aesthethics of PlotProteinOverlap() and PlotPCA(). Changes in version 1.0.0 - The function generateReport() now takes the parameter name_output_file to name the output pdf file. - Added information regarding peptides, and peptides/protein ratio in report tables. - Added the function PlotProteinPeptideRatio() to visualize a comparison between the proteins identified and the ratio Peptide/Proteins among Experiments. Changes in version 0.99.3 - Functions now use a general input resulting from make_MQCombined(). - Shortened lines in the code. - Usage of seq_len rather than 1: ... - Usage of ultiples of 4 spaces for line indents. - Removed LazyData: TRUE. Changes in version 0.99.2 - Added a NEWS.md file to track changes to the package.