El-MAVEN v0.2.4

• Moved AWS login dialog to File menu (#354 )
• Export peak spline area to CSV (#496 )
• Improved EIC for MS/MS data (#487 )
• Error messages in Loess Fit alignment (#328 )
• Beta: Option to align samples to the expected Rt (#514)
• Natural sort for samples and peaks table (#466 )
• Fixed Mac build (#525 525)
• Bug fix in RT line (#553 )
• Bug fix in Report Isotopic Peaks (#453 )
• Fixes in Load/Dump settings feature

El-MAVEN v0.2.3

• Installation and build instructions in README
• Pull Injection order from mzML files (#449 )
• EIC spline exported to clipboard (#474 )
• Fixed issues in "Copy isotopic information" functionality (#469 #468 )
• Fixed crash in isotopes widget
• Disable NA correction by default (#468 )
• Fixed initialization bug in Mass cut off box (ppm/mDa)
• Use gcc5 on Travis CI
• Ionization mode is auto detected on sample upload

El-MAVEN v0.2.2

• Fixed a bug leading to wrong scan in mass spectra widget (#341 )
• Fixed the order of tab control in all dialogs (#217 )
• Added fake compound in case of formula search (#440 )
• Added support for C13 and H2 dual-labeled compounds (#451 )
• Updated --help section in CLI (#458 )
• Made grouping consistent for single and multiple samples (#334 )
• Fixed grouping for full-scan MS2 data (#170 )
• Added another mass accuracy unit, mDa (#137 )
• Fixed an initialization bug in Report Isotopic Peaks (#185 )
• Load and dump settings feature has been introduced (#425 )

El-MAVEN v0.2.1

• Allowed manual linking of SRM transitions to a fragment in LC-MS/MS data (#364)
• Fixed calculation of ppmDiff for labeled peaks in CSV export (#235)
• Fixed a bug leading to non-deterministic merged EIC (#333)
• Added warning for bookmarking the same peak for two compounds (#362)
• Fixed the case of fake peaks (#334)
• Fixed a bug in choosing the correct smoothing algorithm (#391)
• Fixed a bug in C12 parent peak detection (#386)
• Targeted peak picking is available for MS/MS fragments (#406)
• Deleted groups are not exported to JSON (#394)
• CSV export from mzroll has been fixed (#389)
• El-MAVEN installer works for Windows 7 and 10 (#397)
• Added feature testing to compare two versions of El-MAVEN (#339)
• Fixed EIC data for parent and isotope in JSON export (#400)
• Fixed crash on bookmarking peaks from ms1-ms2 text search (#437)
• Fixed non-deterministic EIC pull (#388)
• Proper directory structure implemented (#319)

El-MAVEN v0.2.0

• Added MRM search feature. Search by hyphen-separated precursor and product m/z in the main window search box (#170)
• (Beta Feature) Added a new alignment algorithm- 'Loess Fit'. Option to choose preferred algorithm (#39)
• Debug version has code coverage support for Linux environment (#326)
• README.md has updated installation instructions for Windows, Ubuntu and Mac OS (#194)
• Alignment Polynomial Fit visualization works for loess fit (#312)
• Large files(exe/mzXML) are now stored using Git-lfs (#350)
• CSV reports can be exported from the CLI version.
• CSV export code has been refactored for code re-usability.

El-MAVEN v0.1.5

• README.md has been updated to include code documentation guidelines (#318)
• El-Maven is now supported on Mac OS (#16)
• CONTRIBUTING.md has been updated to include contribution guidelines for users and developers (#323)
• "EIC Processing and Filtering" tab has been renamed to "Group Filtering" in Peaks dialog (#217)
• Fixed a bug in Slicing that set minimum retention time for every EIC to zero (#314)
• Data-dependent MS2 visualization is now supported (#287)
• Sample files have been added to run unit tests during compilation (#314)
• Peaks can be filtered by 'Minimum Signal Baseline Difference' in CLI version (#314)
• PPM range can be adjusted in CLI version (#356)
• Barplot and box plot have been restored (#316)
• CONTRIBUTING.md has been updated to include commit guidelines for developers (#324)
• JSON file format has been fixed
• Refactored JSON export for code re-usability (#347)
• TravisCI has been integrated for continuous testing (#325)
• Failure reports for unit tests are displayed in the terminal after compilation (#320)
• Added License information (#322)
• Option to choose filterline

El-MAVEN v0.1.4

• Use intensity-weighted average for a group to sum EIC over a mass range (#290)
• Keep focus line at expectedRt on bookmarking a peak (#288)
• Fix EIC window display in absence of detected peaks (#285)
• Add "min signal baseline difference" parameter for isotopic peak filtering (#286)
• Add X and Y axis to Scatterplot widget (#297)
• Add formula column in CSV and JSON exports (#229)
• Add injection order information for samples from meta file (#275)
• Add Y axis zoom in/out in EIC display window (#292)
• Keep track of samples used for peak detection (#261)

El-MAVEN v0.1.3

• Provide control over grouping parameters (#151)
• Add minimum signal baseline difference for peak filtering (#153)
• Add separate baseline for every sample (#153)
• Add AreaTopCorrected as new quantitation type (#153)
• Add quantile value for Signal/Blank and Signal/Baseline ratio (#267)
• Move Baseline calculation and smoothing parameters to Options dialog (#217)
• Move Group Rank control to Options dialog (#217)
• Replace input boxes with sliders for quantile filters (#217)
• Change default value for M+n isotope in Options dialog (#276)
• Fix EIC plot of isotopes from mzroll file (#255)
• Annotation of SRMs include retention time information (#260)
• Reduce number of duplicate mass slices during automated feature detection (#152)

El-Maven v0.1.2

EIC extraction when there are multiple peaks in the mass window(#187)
Ftr User can use max or sum (in beta) options in EIC extraction
Ftr Use group rank formula in EIC window (#103)
Highlight peaks based on group rank rather than highest intensity
Ftr m/z information in compound widget (#51)
charge used for pulling EIC is used for calculation of m/z in compound widget
Fix ElMaven can handle multiple charged species (#17)
Read charge from compound database
Ftr Update set information for samples (#228)
User can update the sample information by loading external csv
User can sort the samples by set information
Fix peak table population from mzroll (#249)
Mass slicing algorithm documentation for Untargeted LC-MS data analysis

El-MAVEN v0.1.1

Fix expanding toolbars in application (#41)
Fix save project function (#149)
Fix peak table minimize/restore function (#155)
Fix focus issue in EIC (#169)
Fix export issue (#196)
Fix widget dock issue (#203) (#154)
Fix y-axis scaling (#205)
Update CLI in ElMaven (#230)

• Make a default XML file
• Load an XML file into peakdetectorCLI
• Writing CSV Report
• Fix Load Database File
• Remove unused variables
• Add Limit Scan Parameters
• Add Peak-quantitation type
• Add Quantile Quality Parameter
• Add Quantile Intensity Parameters
• Add Ionization Charge Parameter
• Add option to Save EIC JSON
• Improve console output statements
• Make a header file for PeakDetectorCLI.h
• Refactor processOptions (Parsing Arguments)
• Fix Isotopic Peak Detection
• Input Arguments in CLI using Configuration file
• Introduce classes into PeakDetectorCLI

Fix isotope window (#239)