MS Data Miner / Changelog: Recent posts

1.3.0 (2014-08-15)
• Added: Support for Mascot 2.5. Please see installation guide about how to integrate MDM with Mascot.
• Added: The SRM Selector now supports data from ProteomicsDB.org.
• Updated: P-values are now supported for iTRAQ ratios from Macsot.
• Fixed: Minor bugs and improvements.

1.2.3 (2014-03-28)
• Updated: The reports now include hyperlinks to the respective NCBI protein page for all NCBInr proteins.
• Fixed: The SRM Selector now supports the updated structure of the export files from SRMAtlas.org.
• Fixed: Minor bugs.

1.2.2 (2013-12-19)
• Updated: The speed of the report generator has been improved.
• Updated: The MySQL database has been optimized.
• Fixed: Minor bugs.

1.2.1 (2013-09-20)
• Added: A new PTM analysis tool has been added to the report tool with the following features:
  - Show only proteins and peptides with specific modification.
  - Show only modified positions which have been identified in a certain amount of samples.
  - Show only modified positions identified in peptides with ion scores above a certain threshold.
• Added: Multiple proteins can now be shown in the SRM Selector at the same time and Skyline methods can be created with multiple proteins.
• Added: It is now possible to click on a number in the Venn diagrams to show the corresponding elements.
• Added: Screenshots can now be created based on a list of query numbers under the spectral validation tool.
• Fixed: Minor bugs and improvements.

1.2 (2013-07-09)
• Added: A new SRM Selector tool has been added with the following features:
   - Show peptides for all proteins including values such as highest ion score, number of times oserved, m/z value, charge
     state and most observed modifications.
   - Direct creation of Skyline methods based on selected peptides.
   - Integration with SRMAtlas with support for the following organisms: Human, Mouse & Yeast.
   - Information about tissues and samples in which a protein has been identified.
• Added: The amount of MS/MS queries and assigned queries in Mascot searches has been added to the bottom of all reports under "Search Parameters".
• Changed: The Gene Ontology feature has been moved to the tools section.
• Fixed: Minor bugs and improvements.

1.1.3 (2013-03-20)
• Added: The manual is now available to all users on the login page of MDM.
• Added: The retention time interval is now displayed in the reports for peptides which have been identified multiple times.
• Added: New Tool - A tool has been added to check if Uniprot accessions have become obsolete or have merged into other accessions.
• Added: New Tool - A tool has been added to convert IPI accessions into Uniprot, ENSEMBL or REFSEQ_XP accessions.
• Changed: The import protein list function now also allows importing of no Uniprot proteins as long as the proteins are already in MDM.
• Fixed: Error where Mascot reported extremly large emPAI values. Values larger than 9999 are now reported as 9999.
• Fixed: Minor bugs and improvements.

1.1.2 (2013-01-16)
• Added: Information about the normal distribution for all SILAC ratios is now supported.
• Changed: For Mascot searches, the search title is now used as default subsample name.
• Fixed: Error with exporting label free information from the simple ratio protocol.
• Fixed: Minor bugs.

1.1.1 (2012-12-13)
• Added: Support was added for the following SILAC ratios: L/M, L/H, H/M.
• Added: Organism and tissue information can now be added to a sample.
• Updated: Label free (XIC) quantitation data is now supported for both the average and simple ratio protocol from Mascot Distiller. The two are now available as seperate options in the report generator.
• Updated: Various layout improvements.
• Fixed: The "Highlight proteins" options in the report generater now also works when grouping proteins by subsample.
• Fixed: Minor bugs.

1.1.0 (2012-10-21)
• Added: SILAC support was added for Mascot Distiller data. Labeling is supported with the following ratios: M/L, H/L, M/H.
• Added: iTRAQ support was added for Mascot and ProteinPilot data. Both 4- and 8-plex is supported.
• Added: An option was added to only include tryptic peptides in the Excel reports.
• Added: An option was added to allow showing of identified peptides and cleavage sites in the protein sequence in the reports. The feature is found under the process data of the report generator.
• Added: Modifications absolute position in the protein sequence can now be shown in the reports for Mascot data.
• Added: P1-P4 and P1'-P4' site can now be shown for all peptides in the reports.
• Added: A new tool menu was added with a Venn diagram creator. Diagrams can be created based on samples, subsamples or user defined lists.
• Updated: The import speed of retention times for peptides was improved.
• Updated: The import speed of ProteinPilot data was improved.
• Fixed: Minor bugs.

1.0.2 (2012-07-05)
• Added: All parameters for mascot files are now shown when hovering the mouse over a subsample name in the list of unassociated subsamples.
• Added: In the report generator it is now possible to choose to show only identifications based on e.g. 1 unique peptides in the reports grouped by subsample.
• Added: In the report generator it is now possible to choose to show only peptides with a specific modification.
• Added: Projects can now be archived so that the associated samples and subsamples won't show up in the dropdown lists.
• Added: Mascot spectra screenshots can now be limited in the spectra screenshot generator so that only screenshots of peptides with a specific modification is generated
• Updated: The import speed of retention times for peptides was improved (2.4x speed improvement) and is now not default imported.
• Updated: The Excel export was optimized and file size was reduced by up to 20%.
• Fixed: Minor bugs.

1.0.1 (2012-04-30)
• Added: Samples can now be grouped into Projects in the samples menu.
• Added: Support was added for peptide information from ProteinPilot.
• Added: MDM Automatically checks for updates from Sourceforge and informs users about new versions on the login page.
• Added: P-value is now listed for the subsamples in the samples menu. All other parameters are shown when hovering the mouse over a subsample name.
• Added: Retention time for peptides is now collected when importing Mascot data. The retention time can be included in the exported reports under peptides.
• Updated: The spectra validation tool can now be used to validate all proteins instead of just proteins identified based on one unique peptide. MDM automatically recalculates # matches, # significant matches, # sequences, # significant sequences, # unique peptides and protein coverage after removing a peptide.
• Updated: The total samples & subsamples added for the past 14 days is now shown under statistics.
• Fixed: Minor bugs when importing Mascot data.... read more