Integrative analysis of multimodal mass spectrometry data in MZmine 3

3 Pág.We thank Christopher Jensen and Gauthier Boaglio for their contributions to the MZmine codebase. We thank Jianbo Zhang and Zachary Russ for their donations to MZmine development. The MZmine 3 logo was designed by the Bioinformatics & Research Computing group at the Whitehead Institute for Biomedical Research. T.P. is supported by Czech Science Foundation (GA CR) grant 21-11563M and by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement 891397. Support for P.C.D. was from US NIH U19 AG063744, P50HD106463, 1U24DK133658 and BBSRC-NSF award 2152526. T.S. acknowledges funding by Deutsche Forschungsgemeinschaft (441958208). M. Wang acknowledges the US Department of Energy Joint Genome Institute ( https://ror.org/04xm1d337 , a DOE Office of Science User Facility) and is supported by the Office of Science of the US Department of Energy operated under subcontract No. 7601660. E.R. and H.H. thank Wen Jiang (HILICON AB) for providing the iHILIC Fusion(+) column for HILIC measurements. M.F., K.D. and S.B. are supported by Deutsche Forschungsgemeinschaft (BO 1910/20). L.-F.N. is supported by the Swiss National Science Foundation (project 189921). D.P. was supported through the Deutsche Forschungsgemeinschaft (German Research Foundation) through the CMFI Cluster of Excellence (EXC-2124 — 390838134 project-ID 1-03.006_0) and the Collaborative Research Center CellMap (TRR 261 - 398967434). J.-K.W. acknowledges the US National Science Foundation (MCB-1818132), the US Department of Agriculture, and the Chan Zuckerberg Initiative. MZmine developers have received support from the European COST Action CA19105 — Pan-European Network in Lipidomics and EpiLipidomics (EpiLipidNET). We acknowledge the support of the Google Summer of Code (GSoC) program, which has funded the development of several MZmine modules through student projects. We thank Adam Tenderholt for introducing MZmine to the GSoC program.Peer reviewe

mzmine/mzmine3: Latest Development Build

<h2>Commits</h2> <ul> <li>ed17f3c: Increment patch version (SteffenHeu)</li> <li>6edef2d: add toString method to simple row group (robinschmid) <a href="https://github.com/mzmine/mzmine3/pull/1623">#1623</a></li> <li>a155520: Merge pull request #1623 (Robin Schmid) <a href="https://github.com/mzmine/mzmine3/pull/1623">#1623</a></li> </ul&gt

mzmine/mzmine3: Latest Development Build

<h2>Commits</h2> <ul> <li>f9855dd: Increment patch version (SteffenHeu)</li> <li>8f1e930: Update README.md (Robin Schmid)</li> </ul&gt

mzmine/mzmine3: Latest Development Build

<h2>Commits</h2> <ul> <li>5707d82: Increment patch version (robinschmid)</li> <li>b5fe0e3: remove record pattern matching use (robinschmid) <a href="https://github.com/mzmine/mzmine3/pull/1582">#1582</a></li> <li>48eb4b9: jdk21 (robinschmid) <a href="https://github.com/mzmine/mzmine3/pull/1582">#1582</a></li> <li>30c4c73: update mockito and remove mockito inline (robinschmid) <a href="https://github.com/mzmine/mzmine3/pull/1582">#1582</a></li> </ul&gt

mzmine/mzmine3: Latest Development Build

<h2>Commits</h2> <ul> <li>9c6dcc0: Increment patch version (robinschmid)</li> <li>dad3e84: new binary search options (robinschmid) <a href="https://github.com/mzmine/mzmine3/pull/1568">#1568</a></li> <li>2d50abf: binary search tests (robinschmid) <a href="https://github.com/mzmine/mzmine3/pull/1568">#1568</a></li> <li>9104f32: simplify if as upperSearchPoint only needs to be smaller than lower to fail (robinschmid) <a href="https://github.com/mzmine/mzmine3/pull/1568">#1568</a></li> <li>cbac1a9: use index range to group MS2 in MALDI (robinschmid) <a href="https://github.com/mzmine/mzmine3/pull/1568">#1568</a></li> <li>f634424: fix IndexRange.copyRemoveRange (robinschmid) <a href="https://github.com/mzmine/mzmine3/pull/1568">#1568</a></li> </ul&gt

mzmine/mzmine3: Latest Development Build

<h2>Commits</h2> <ul> <li>872e4e8: Increment patch version (ansgarkorf)</li> <li>72543f5: review, deactivate ctrla in feature table (SteffenHeu) <a href="https://github.com/mzmine/mzmine3/pull/1570">#1570</a></li> </ul&gt

mzmine/mzmine3: Latest Development Build

<h2>Commits</h2> <ul> <li>9c22431: Increment patch version (ansgarkorf)</li> <li>5e7fb17: fix mirror plot labels (robinschmid) <a href="https://github.com/mzmine/mzmine3/pull/1573">#1573</a></li> <li>a60c447: fix library to feature list for network view (robinschmid) <a href="https://github.com/mzmine/mzmine3/pull/1574">#1574</a></li> <li>aa443a1: default to base peak mz for missing precursor mz, e.g., MS1 scans (robinschmid) <a href="https://github.com/mzmine/mzmine3/pull/1574">#1574</a></li> </ul&gt

mzmine/mzmine3: Latest Development Build

<h2>Commits</h2> <ul> <li>b73ae8f: Start mass detector remodel (robinschmid) <a href="https://github.com/mzmine/mzmine3/pull/1615">#1615</a></li> <li>2214d89: Increment patch version (ansgarkorf)</li> <li>bef12b3: Remodel mass detection modules by incorporating parameters (robinschmid) <a href="https://github.com/mzmine/mzmine3/pull/1615">#1615</a></li> <li>96ba1e3: correct feature detection test. was not using advanced import so turn off (robinschmid) <a href="https://github.com/mzmine/mzmine3/pull/1615">#1615</a></li> </ul&gt

mzmine/mzmine3: Latest Development Build

<h2>Commits</h2> <ul> <li>d963958: add iintest ions, fix ion type in csv search (Steffen Heuckeroth) <a href="https://github.com/mzmine/mzmine3/pull/1610">#1610</a></li> <li>b2a64df: fix notation (Steffen Heuckeroth) <a href="https://github.com/mzmine/mzmine3/pull/1610">#1610</a></li> <li>71785a0: fix ion parsing for special cases with electrons (robinschmid) <a href="https://github.com/mzmine/mzmine3/pull/1610">#1610</a></li> <li>0c433cb: Merge remote-tracking branch 'SteffenHeu/add-more-ions-to-iintest' into fork/add-more-ions-to-iintest (robinschmid) <a href="https://github.com/mzmine/mzmine3/pull/1610">#1610</a></li> <li>25c5f53: add special ion case (robinschmid) <a href="https://github.com/mzmine/mzmine3/pull/1610">#1610</a></li> <li>b01e966: Merge remote-tracking branch 'mzmine/master' into add-more-ions-to-iintest (Steffen Heuckeroth) <a href="https://github.com/mzmine/mzmine3/pull/1610">#1610</a></li> <li>0b4a328: Merge remote-tracking branch 'origin/add-more-ions-to-iintest' into add-more-ions-to-iintest (Steffen Heuckeroth) <a href="https://github.com/mzmine/mzmine3/pull/1610">#1610</a></li> <li>26f90c5: handle null in number parsing (robinschmid) <a href="https://github.com/mzmine/mzmine3/pull/1610">#1610</a></li> <li>96a18f4: Merge remote-tracking branch 'SteffenHeu/add-more-ions-to-iintest' into fork/add-more-ions-to-iintest (robinschmid) <a href="https://github.com/mzmine/mzmine3/pull/1610">#1610</a></li> <li>b72438d: Increment patch version (ansgarkorf)</li> </ul&gt