server-v3.4

Better Prophane compatibility, fixed UI bug

server-v3.3

MPA-Server release for Conda compatibility.

portable-v2.0.1

Supplementary MPA-Unipept

MPA Portable 2.0

MPA Portable version 2.0 has been released with the following features:

• The graphical user interface now supports a direct connection to the Unipept (https://unipept.ugent.be/) web interface: identified peptides are directly mapped to the Unipept service (using the MPA Export menu --> Export peptides to Unipept)
• UniProt JAPI was updated to the version 1.0.28

MPA Portable 1.8.1

MPA Portable version 1.8.1 has been released with the following update:

• UniProt JAPI was updated to the latest version 1.0.22 (fixing errors occurring during the retrieval of UniProt meta-information)

MPA Portable 1.8.0

MPA Portable version 1.8.0 has been released with the following features/bugfixes:

• MS-GF+ parameter for fragmentation method (CID, ETD, HCD) can be chosen on the command line.
• UniProt JAPI was updated to the latest version 1.0.16 (fixing errors occurring during the retrieval of UniProt meta-information)
• Batch scripts are now available in the main folder of the software.
• Various bugfixes and improvements within the code.

MPA Portable 1.5.0

MPA Portable version 1.5.0 has been released with the following new features:

• Added "Import MPA Experiment" feature: saved experiment files (*.mpa) can now be loaded into into a project
• Updated "Export MPA Experiment" feature: experiment files (*.mpa) are stored together with the original MS/MS spectra
• Added "Update UniProt Entries" feature (see MetaProteomeAnalyzerCLI for details)
• Various bugfixes and GUI improvements

MPA Portable 1.9.0

MPA Portable version 1.9.0 has been released with the following features/bugfixes:

• Fully moved the MPA project to Maven to make it easier to build packages and include external dependancy libraries
• Performed various bugfixes to make MPA run again
• UniProt JAPI was updated to the latest version 1.0.26 (fixing errors occurring during the retrieval of UniProt meta-information)

MPA Portable 1.7.0

MPA Portable version 1.7.0 has been released with the following new features:

• Added taxon-based two-step searching feature (in addition to the protein-based strategy).
• MapDB was updated to the latest version (ver. 3.0.5) to accelerate the peptide indexing.
• Peptide indexing is now available as optional feature on the command line.
• Disabled emPAI and NSAF quantification features in the GUI to accelerate the results retrieval.

MPA Portable 1.6.0

MPA Portable version 1.6.0 has been released with the following new features:

• Added new import function for mzIdentML files: this feature supports the re-analysis of result identification data stored in mzIdentML format.
• Added new Import menu which contains the import function for "MPA Experiment" (see Release version 1.5.0).
• Added the feature to import MPA experiment files without requiring the corresponding MGF files.
• Added the indexing of peptide sequences for FASTA databases: this feature allows to retrieve all protein identifications contained in the reference proteomes (and more than the default hits suggested by the search engines).