release 2.1.35

Changes:

• The annotation of compounds with metal complexes has been improved.
• The performance of Compound Search has been improved.
• Annotated Features Overview - retention time is now listed for LC-MS data, the width of columns can be modified.
• An average spectrum can now be calculated for LC-MS data in Chromatogram Window and the peaks can be annotated.
• The ids of groups were replaced by names in Define Samples and Calibration Curve dialog.
• The concentrations of compounds can now be visualized in the dependency on the sample collection time.
• Some other minor bugs and performance issues were fixed and minor improvements were made.

release 2.1.21

Changes:

• Quantification of compounds in LC-MS datasets is now possible.
• "Annotated Features Overview" added (a table of all features matched in all LC-MS files).
• "Simulate Isotopic Pattern" feature added.
• "Calculate Molecular Formula" feature added.
• The names corresponding to molecular formulas of compounds identified in "Compound Search - MS, LC-MS, MSI" mode can now be searched in PubChem.
• The range of retention time can now be limited in the settings dialog if LC-MS data is processed.
• Retention time of individual database compounds can also be limited if LC-MS data is processed.
• "Minimum Intensity of Highest Peak in Isotopic Pattern" parameter was added into the Settings dialog.
• "54Fe/56Fe Ratio" parameter was added into the Settings dialog.
• Line/Profile mass spectra can now optionally be converted by CompassXtract from baf files.
• Waters data support improved.
• EIC chromatogram is now visible by default.
• Calculation of FDRs (LC-MS and MSI data) can optionally be disabled.
• Copy to clipboard function (CTRL+C) improved in Building Block, Sequence/Compound, and Modification editors.
• Remove duplicate rows feature added in Sequences/Compounds Editor.
• Export matched formulas to a compound database - feature available in "Summary Table of Matched Peaks" and "Annotated Features Overview" if "Compound Search - MS, LC-MS, MSI" mode was used.
• Results files (*.res) are now backwards compatible (starting from version 2.0.8).
• Data processing tab added in Preferences dialog.
• Compounds in NP Atlas and COCONUT can now be referenced from Sequence/Compound Editor.
• Bookmarks toolbar was added and corresponding tab was fixed in Preferences dialog.
• Unused parameters are now automatically hidden in the Settings dialog.
• Multiple LC-MS files can now be processed in a batch.
• Multiple threads can now be used if LC-MS or MSI data are processed.
• Image fusion improved:
  • Current configuration of layers can now be loaded/saved.
  • Open image function was improved.
  • Import dialog was added to open a batch of microscopy images FEI (SEM) / Leica (optical and fluorescence).
  • Optical and fluorescence microscopy images can now be opened directly from *.lif files (Leica).
  • Horizontal and vertical flip feature added for microscopy images.
  • Name and magnification is now visible for every microscopy layer.
  • Navigation buttons were added to browse microscopy layers (Previous, Next).
  • Maximum number of microscopy layers was increased to 200.
  • A dropdown menu was added to change the navigation layer of any microscopy layer.
  • Keep aspect ratio feature added when resizing a region (CTRL + resize by mouse).
  • Clear all/individual layers features added.
• Some other minor bugs and performance issues were fixed and minor improvements were made.

release 2.0.8

Changes:

• Custom ions are now supported for MS, LC-MS, and MSI data.
• Global preferences dialog added (custom ions, default directories, default URLs).
• Chromatogram window improved - names/molecular formulas of matched compounds are now reported.
• Support of fine isotopic patterns of metals improved.
• New scoring function added - weighted ratio of matched peaks.
• m/z values of unmatched theoretical peaks in single spectrum detail window can now be focused in a spectrum using a double-click.
• Bug fixed: intensities in chromatogram window and CrossVis were summed if the same experimental peak was matched by multiple compounds.
• A bug was fixed when peaks of scrambled ions were generated.
• Link to PubChem was fixed.

release 2.0.0

Changes:

• Compound search mode added (a database-free search mode for MS1, LC-MS, and MSI data).
• Fragmentation of metabolites is now supported (peptide type "Other" in MS/MS mode).
• A list od neutral losses can now be defined for individual building blocks.
• The databases of blocks were updated to a new file format (the column neutral losses was added).
• Spectrum detail window can now be opened direcly from chromatogram or image window (CrossVis) by a double-click.
• Filter options improved - main window, summary table of matched peaks, and editors (building blocks, sequences/compounds, and modifications).
• Processing of Waters data improved and visualization of profile data added.
• Visualization of profile mzML/Thermo raw files added and a bug fixed during profile data processing.
• Retention time is now reported for LC-MS data.
• Minimum number of spectra can now be defined for LC-MS and MSI data.
• Minimum number of matched ions can now be defined for MS, LC-MS, and MSI data.
• New parameters added: Basic Formula Check, Advanced Formula Check, N/O Ratio Check, Isotope m/z Tolerance, and Isotope Intensity Tolerance.
• Percentage contributions of peak components (e.g. 13C, 17O) are now reported if theoretical isotopic patterns are calculated.
• Copy to clipboard function (CTRL+C) improved in spectrum detail window, main window, and summary table of matched peaks (multiple rows and columns can be selected in the table).
• Visualization of mass spectra fixed (occasional flashing).
• A bug fixed - existing items in the list of neutral losses were not editable if the settings dialog was re-opened.
• A bug was fixed when too many combinations of neutral losses were generated.
• Internal ions can now be generated for branch-cyclic peptides.
• DOI can now be used as a reference in a compound/sequence database.
• [M+Cl]- ion added in MS mode.
• Link to BBDGNC added.
• zlib compression is now supported in mzML files.
• Some other bugs were fixed and minor improvements were made.

release 1.3.1

Changes:

• Spectrum detail window improved:
  • Profile spectra can now be visualized.
    • Bruker's baf files (Windows only)
    • imzML
  • Visualization of mass spectra improved.
  • Hide labels of peaks feature added.
  • Mouse wheel function improved.
  • Summary formulas of experimental peaks are now reported also in MS/MS mode.
  • An experimental peak can now be focused in using a double-click.
• Chromatogram - visualization and mouse wheel function improved.
• Summary Table of Matched Peaks - an experimental peak can now be focused using a double-click.
• "Compare Peaklist with Database - MS/MS data" mode - a bug fixed; different theoretical spectra with the same score were reported only once.
• LC-MS/MS data - all spectra in a dataset are now compared with a theoretical spectrum of a searched sequence if "Compare Peaklist(s) with Spectrum of Searched Sequence" mode is used (the parameter "Scan no." is not used in this mode).
• Settings dialog - layout fixed for macOS.
• FileConverter - collision of filenames between OpenMS and Xcalibur fixed.

release 1.2.748

26.2.2018

Changes:

• A custom list of neutral losses can now be defined for MS, MSI and MS/MS data.
• Details of MS/MS spectra improved - matched peaks can now be filtered using a name of a ion series or using name of a neutral loss.
• Settings dialog improved:
  • "Neutral Losses" - a modifiable list added.
  • "Maximum Number of Combined Losses" - settings added.
  • "Report Unmatched Theoretical Peaks" - checkbox added; performance improved if unchecked.
  • "m/z Error Tolerance for Deisotoping" - obsolete feature removed.
  • "Remove Hits of Fragments without Hits of Parent Fragments" - obsolete feature removed.
  • Obsolete scoring functions removed.
• Unmatched theoretical isotope patterns can now be reported in MS, MSI and MS/MS mode.
• Memory performance was improved.
• OpenMS 2.3 is now supported.
• Thermo raw files are now supported.
• mzML support improved.
• [M]+, [M]- ions added.
• Bug fixed: the number of electrons was wrong if the m/z ratio of negative ions was calculated in "Generate Full Isotope Patterns" mode.

release 1.2.660

15.12.2017

Changes:

• De novo sequencing improved - sequence candidates with the same score and identical path in the de novo graph are now reported only once.
• Summary formulas of fragment ions are now reported.
• Fine isotope patterns of fragment ions are now generated.
• Visualization of mass spectra and chromatogram improved - they can be shifted left/right by mouse now.
• The list of peaks in a spectrum detail window can now be filtered using a ring break-up point (cyclic peptides) or linearized sequence type (branched peptides).
• CrossVis - support of microscopy images fixed; image export fixed; pixel width and height fields added.
• Summary Table of Matched Peaks - calculation of statistics fixed.
• Multiply dehydrated and deamidated fragment/precursor ions are now reported.
• imzML support improved.
• CompassXPort support improved.
• [M+Si-3H]+, [M+Si-4H+Na]+, [M+Si-4H+K]+, and [M+Si-5H]- ions added.
• Some minor bugs were fixed and performance was improved.

release 1.2.495

22.6.2017

Changes:

• Image Window replaced by CrossVis tool (MALDI-MSI and DESI-MSI data can now be correlated with histology and microscopy images).
• Waters raw data folders can now be processed (Windows only).
• [M+Na-2H]-, [M+K-2H]-, and [M+NH4]+ ions added.
• Single spectra can now be opened also from the Summary Table of Matched Peaks using Enter key or a row double click.
• Filter options in Main Window, Summary Table of Matched Peaks, Building Blocks Editor, Sequence Database
• Editor and Modifications Editor improved.
• Minimum Threshold of Absolute Intensity option added into the Settings Dialog.
• Minimum Pattern Size option added into the Settings Dialog.
• Generate Permutations of Building Blocks option removed from Settings Dialog; the feature is now always enabled.
• Scores and FDRs of matched isotope patterns are computed for MS/MSI data.
• Summary Table of Matched Peaks - exported statistics improved.
• Show Isomers feature now affects Main Window, Summary Table of Matched Peaks, Spectra Details, De Novo Graph window, and HTML export.
• Single spectrum detail window and visualization of single spectra improved.
• Ppm error is now reported as a positive/negative number.
• Chromatogram window added.
• Icon sizes increased.
• Some bugs were fixed and some other minor improvements were made.

release 1.2.192

3.10.2016

Changes:

• mzML file format support fixed.
• LC-MS/MS spectra support added - id of a scan can now be entered in the settings dialog.
• Absolute intensities of peaks are now reported.
• Summary Table of Matched Peaks improved - statistics of matched ions can now be exported.
• Image Window improved - number of selected points, color scale, average intensity, median intensity, and searched text are reported.
• Full isotope patterns of compounds can now be generated (MS and MSI data).
• Visualization of Waters imzML datasets is now supported.
• Some bugs and performance issues were fixed and some other minor improvements were made.

release 1.1.570

19.5.2016

Changes:

• New features have been added in the building blocks editor, sequence database editor and modifications editor - create a new database, import a database, un/select all rows.
• Menubars have been included in the building blocks editor, sequence database editor, modifications editor and summary table of matched peaks.
• Some bugs and multiple performance issues have been fixed.
• Some keyboard shortcuts have been fixed.
• The support of biometals and polyketide siderophores have been improved.
• Group id is now reported for de novo sequence candidates.
• Imaging mass spectra and imzML data format are now supported.