NEWS.md

In BioAlvaro/ProteoMS: Quality Control of Protemics Data

MQmetrics 0.99.2

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

MQmetrics 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.

MQmetrics 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.

MQmetrics 1.1.1

• Added pagination to PlotiRT() and PlotiRTScore().
• Updated vignette style to Bioconductor's.
• Improved aesthethics of PlotProteinOverlap() and PlotPCA().

MQmetrics 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().

MQmetrics 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).

MQmetrics 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.

MQmetrics 1.1.5, 13/09/2021

• 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.

MQmetrics 1.1.6, 06/10/2021

• Bug fixed: If a table was missing, the report was not generated.

MQmetrics 1.1.7, 07/10/2021

• Removed parentheses from the news that was causing issues in Bioconductor.

MQmetrics 1.1.8, 08/10/2021

• Fixed test that was resulting in error duet to version 1.1.6 updated way to read the files.

MQmetrics 1.3.1 03/01/2022

• 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.

MQmetrics 1.3.2 03/01/2022

• Reporthing the fixed Modifications if the mqpar.xml is present.

MQmetrics 1.3.3 10/01/2022

• Removed unused dependency.

BioAlvaro/ProteoMS documentation built on Jan. 12, 2022, 9:46 a.m.