@novak-jiri novak-jiri released this Nov 8, 2018 · 2 commits to master since this release

Assets 3

Changes:

  • minimum feature size can now be defined for LC-MS data
  • all ions of a compound must be matched (e.g. [M+H]+ and [M+Na]+) feature added
  • performance of brute force fragmentation improved
  • internal ions can now be generated for branch-cyclic peptides
  • copy to clipboard function (CTRL+C) fixed in the main window and summary table of matched peaks
  • DOI can now be used as a reference in a compound/sequence database
  • [M+Cl]- ion added in MS mode
  • Waters data support fixed

@novak-jiri novak-jiri released this Sep 20, 2018 · 4 commits to master since this release

Assets 3

Changes:

  • feature added: percentage contributions of peak components (e.g. 13C, 17O) are now reported if theoretical isotopic patterns are calculated
  • feature added: copy to clipboard function (CTRL+C) improved in spectrum detail window (multiple rows and columns can be selected in the table)
  • bug fixed: existing items in the list of neutral losses were not editable if the settings dialog was re-opened
  • bug fixed: an error was fixed when too many combinations of neutral losses were generated
  • a few bugs were fixed if profile mass spectra were processed

@novak-jiri novak-jiri released this May 16, 2018 · 7 commits to master since this release

Assets 10

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.

@novak-jiri novak-jiri released this May 11, 2018 · 10 commits to master since this release

Assets 8

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.

@novak-jiri novak-jiri released this Feb 21, 2018 · 21 commits to master since this release

Assets 8

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.

@novak-jiri novak-jiri released this Feb 21, 2018 · 22 commits to master since this release

Assets 8

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.

@novak-jiri novak-jiri released this Feb 21, 2018 · 23 commits to master since this release

Assets 8

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.

@novak-jiri novak-jiri released this Feb 21, 2018 · 24 commits to master since this release

Assets 8

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.

@novak-jiri novak-jiri released this Feb 21, 2018 · 25 commits to master since this release

Assets 8

15.12.2015

Changes:

  • Support of siderophores and polyketides improved.
  • Feature added - summary table of matched peaks.
  • Feature added - cancel buttons have been added into some progress dialogs.
  • Bug fix - program crashed from time to time when combinations of building blocks were generated.
  • Bug fix - detection of branch-cyclic NRPs using series D) and H) fixed.

@novak-jiri novak-jiri released this Feb 21, 2018 · 26 commits to master since this release

Assets 8

21.9.2015

Changes:

  • Peaks in a spectrum detail window are now reported in a table.
  • The table of peaks can be exported into a csv file.
  • Columns containing real numbers are now sorted correctly.
  • HTML export was improved.
  • Peaklist from multiple scans can now be processed in MS mode.
  • Support of identification of NRP siderophores added.
  • Support of linear and cyclic polyketide siderophores added.
  • Support of common biometals added (MS and MS/MS mode).
  • Some keyboard shortcuts were added in the building blocks editor, sequence database editor, modifications editor, draw peptide tool, main window, settings dialog, and de novo graph window.
  • Terminal modifications are now reported in spectra detail windows.
  • Links to Norine and Smiles2Monomers added.
  • A compatibility issue with CompassXPort was fixed.
  • Some bugs were fixed and minor improvements were made.