2023

August 1, 2023

  • Added fields to transformation settings aspect of data import filter that allows users to reverse a log transformation already applied to the uploaded data. This is helpful in cases where a multimodal distribution of quantitative values is found in cases where phosphorylation sites observed in a variety of multiplicity states are aggregated.

  • Added extra filtering steps to column headers of uploaded files. These remove incompatible header elements introduced by Perseus software.

  • Added data import presets and wizard for data generated with FragPipe.

June 3, 2023

  • Added support for mouse and rat phosphoproteomes.

  • Overhauled user interface.

  • Simplified data upload wizard.

  • Fixed bug that prevent display of user feedback for failed analyses.

  • Added database status page.

  • Removed redundant analyses.

2022

February 9, 2022

  • Added user feedback in cases where cluster map plots fail due to too few points.

  • Fixed bugs in zoom function of certain plots.

January 31, 2022

  • Global protein identification lists can now be uploaded to provide additional upstream kinase detection data.

  • Added ability to differentially select either up or down regulated sites from volcano plots.

  • Integrated BioGRID interaction database.

  • Added AlhpaFold protein structe predictions to substrate explorer.

January 28, 2022

  • Added ability to differentially select either up or down regulated sites from volcano plots.

2021

December 15, 2021

  • Fixed bug that prevented downloading volcano plot data as CSV.

December 10, 2021

  • Added basic API functionality. See here for details

  • Improved structure of import parameters file

November 1, 2021

  • Improved post-analysis error notifications

  • Added variance stabilising normalisation option

  • Added group creation metadata to parameter file

  • Added group and sample name validation procedures

October 19, 2021

  • Protein group unwrapping now performed post-statistical analysis

  • Cleaned up JS dependencies

  • Default sample alias is now that produced by removing the largest prefix that is common to all selected quantification columns.

October 18, 2021

  • Added option for quantile normalisation in data import wizard. This is achieved using the 'normalizeBetweenArrays' function in LIMMA.

  • Added downloadable parameter file that contains data import settings. This can be accessed in the setup wizard, summary and downlad pages.

  • Multiple entries for the same phosphoarylation site (i.e. where protein ID, residue and site are identical on multiple rows) are now summed automatically. These are assumed to be separate entries arising from multiplicity of sites.

  • Improved error reporting on initial data upload.

  • Implemented rough initial data validation procedure to column assignment step of import wizard.

  • Fixed bug that caused data import to fail when column headers contained certain non-alphanumeric characters.

October 14, 2021

  • Implemented upgrades to data import wizard column selection and sample grouping UI.

October 13, 2021

  • Fixed a number of bugs that allowed for multiple submissions with the same dataset ID.

  • Fixed bug that resulted in missing metadata when a previously analysed dataset was restored via a retained dataset ID.

October 7, 2021

  • Changed data retention policy. Uploaded datasets are now automatically erased after 15 days.

  • Added license page links.

September 20, 2021

  • Added PDB structure viewer to substrate explorer page.

  • Updated citations.

September 17, 2021

  • Implemented statistical analysis methods from LIMMA

    • p-values displayed throughout Phosphomatics are now those derived from moderated t-tests.

  • Added options to download SVG images of data plots

  • Edited default MaxQuant LFQ import column assignments

  • Added function to unwrap protein groups by default

  • Added missing value visualisations to data import wizard

  • Updated display configuration for substrate quantitation plots

  • Updated display configuration for kinase-substrate quantitation plots

August 10, 2021

  • Fixed bug on kinase-substrate relationship pages that prevented loading of STRING interaction networks on some browsers.

May 28, 2021

  • Implemented performance improvements to initial data processing step.

  • Fixed bug in setup wizard 'Predefined group comparisons' where p-val and fold change column headers were reversed.

  • Fixed setup wizard bug wherein data columns labelled 'quant', but not assigned to sample groups were included in analyses. These are now excluded.

  • Fixed y-axis diaplay bug on summary page cluster map