Feature - mspp Wiki - mspp

Feature

Open-source edition of Mass++ has almost functionalities of previous binary edition of Mass++. But some important functions such as peak detection which are necessary for proteome data analysis. Therefore, we show feature comparison between open-source edition and previous binary edition of Mass++.

Feature Comparison

Component	Category	Plug-in name	Description	Binary Edition	OSS Edition
	Document	-	Release note, etc.	IN
		-	User's manual	IN
	File I/O	File I/O	File R/W basic function	IN	IN
		mzXml I/O	R/W mzXML files	IN	IN
		mzml I/O	R/W mzML files	IN	IN
		AIA Input	Reading AIA (netCDF) files	IN	IN
		MSB I/O	R/W MSB files	IN	IN
		Text I/O	R/W plain text files	IN	IN
		Png Output	Writing PNG files	IN	IN
		Shimadzu Kratos AXIMA	Reading Shimadzu/Kratos AXIMA data files	IN
		Shimadzu Lcms Input	Reading Shimadzu LCMS data files	IN	IN(need vendor's dll to build
		Ab Qstar Input	Reading ABSciex Analyst/AnalystQS data files	IN
		Watewrs Input	Reading Waters MassLynx data files	IN
		Thermo I/O	Reading ThermoFisher Xcalibur data files	IN	Planned(See Milestone)
		Agilent Input	Reading Agilent MassHunter data files	IN
	Database	DB Manager	Internal database manager	IN	IN
		SQLite	Database manager for SQLite	IN	IN
		PostgreSQL	Database manager for PostgreSQL	IN	IN
	Network	Http Proxy	Configurating HTTP Proxy	IN	IN
	Viewer	MDI Child Frame	MDI window manager	IN	IN
		Spectrum & Chromatogram Window Mode	Cordinator for Spectrum window and Chromatogram window	IN	IN
		Profile Canvas	Displaying single window	IN	IN
		Overlapping Canvas	Displaying overlapping windows	IN	IN
		Vertical Box Canvas	Displaying windows in stacked format	IN	IN
		Profile Drawer	Drawing waveform	IN	IN
		Scale Drawer	Drawing axes and scales	IN	IN
		Profile Range	Setting spectrum/chromatogram ranges	IN	IN
		Datamap Canvas	Configuring heat map area	IN	IN
		Datamap Drawer	Drawing heat maps	IN	IN
		Sample 3D View	Drawing 3-D graphs	IN	IN
		Data Map Range	Display range manager for data maps	IN	IN
		First View	Display manager for opened data	IN	IN
	Spectrum/Chromatogram	Select Range	Sending spectrum/chromatogram information and specified ranges to plug-ins	IN	IN
		Magnifying View	Magnifying specified area in the spectrum	IN	IN
		Spectrum Changer	Changing displeyed spectrum	IN	IN
		Spectrum Precursor Product Changer	Displaying precursor/product ion spectrum	IN	IN
		Chromatogram Operation	Generating Mass Chromatograms/Base Peak Chromatograms	IN	IN
		Spectra Search	Searching spectra	IN	IN
		Raw Waveform	Displaying raw waveform data	IN	IN
		Peak Waveform	Displaying peaks on waveforms	IN	IN
	Data Map	Data Map Filter	Filtering data for data map	IN	IN
	Pane	Sample Tree View	Sample Tree pane manager	IN	IN
		Details View	Properties pane manager	IN	IN
		XYData View	Points/Peaks pane manager	IN	IN
		Spectra Grid View	Filtered Spectra pane manager	IN	IN
		Log View	Diagnostic Log pane manager	IN	IN
	Peaks	Peak Picking	Detecting peaks	IN	IN
		GOZAN	Peak detection by MWD algorithm	IN
		Centroid Mode Labeling	Peak detection by Centroid mode	IN	IN
		Local Maximum Labeging	Peak detection by Local maximum mode	IN	IN
		GION	Peak detection by GION algorithm	IN
		Multi Algorithm Labeling	Peak detection by multiple algorithm	IN	IN
		API Peak Detection	Application Programing Interface for peak detection	IN	IN
		Spec Peak Filter Number Of Peaks	Selecting the specified number of highest peaks	IN	IN
		MRM 3D	2-dimensional peak detection for MRM data	IN	IN
		Default Charge	Configurating charge setting function	IN	IN
		Simple Charge Detect	Detecting ion charges with isotopic peaks	IN	IN
		Intensity Rate Charge Detector	Detecting ion charges with MS/MS spectrum distibution	IN	IN
		Peak Search	Searching peaks	IN	IN
		Peaks I/O	R/W peak data	IN	IN
		Peak Edit	Editing peak properties	IN	IN
		Mspeaks	Peak detection with Matlab mspeaks function (32bit only)	IN	IN
		Mslowess	S/N filtering function with Matlab mslowness function	IN	IN
		Peak Label Drawer	Drawing peak labels	IN	IN
	Quantitation	Matrix View	Displaying a peak matrix	IN	IN
		AB3D	Peak detection algorithm AB3D for quantification	IN	IN
		AB3D (2)	Program files for AB3D algorithm	IN	IN
		Labeling And Merge	Finding peak position by peak detection	IN	IN
		Merged Spectrum Peaks	Finding peak position with spectrum peaks	IN	IN
		MRM Peak Finder	Finding peak position for MRM data	IN	IN
		Peak Positions File Import	Importing peak position list	IN	IN
		Simple Peak Position Appender	Manually specifying peak positions	IN	IN
		Neighbor Peaks	Peak value calculation with neighbor peaks	IN	IN
		Commons Math	Statistic analysis with Commons Math library	IN	IN
		U Test	Mann-Whitney's u-test	IN	IN
		Matrix Group Plot	Plotting group distribution of intensities/areas	IN	IN
		Matrix Overlapping View	Displaying overlapping waveforms	IN	IN
		Basic Scaling	Simple normalization of peak intensities	IN	IN
		Matrix Peaks Merge	Merging neighbor peaks on peak matrix	IN	IN
	Identification	Identification	Identification function manager	IN	IN
		Mascot Search	Searching sequence database by Mascot	IN	IN
		X Tandem	Searching sequence database by X!Tandem	IN	IN
		Mass Bank	Support function for MassBank	IN	IN
		MSn Search	Search engine with MSn spectra	IN
		Mascot PMF For LCMS	Mascot PMF search for LC-MS	IN	IN
		TPP	TPP tool wrapper	IN	IN
	Basic Data Manipulation	Baseline Subtraction	Subtracting baseline values from spectrum waveforms	IN	IN
		ABC Baseline Detection	Baseline detection algorithm ABC	IN	IN
		BLT Baseline Detection	Baseline detection algorithm BLT	IN
		Linear Baseline Detection	Baseline detection algorithm Linear	IN	IN
		Background Subtraction	Subtracting backgroud signals from spectrum waveforms	IN	IN
		Filter	Filtering waveforms	IN	IN
		Linear Filter	Filtering waveforms with Linear-mode	IN	IN
		Window Filter	Filtering waveforms with window search	IN	IN
		Wavelet Analysis	Wavelet analysis	IN
		Mz Range Filter	Filtering waveforms with m/z ranges	IN	IN
		Msbackadj Baseline Detection	Detecting baseline with Matlab msbackadj function	IN	IN
		Operation Manager	History recorder of waveform manipulation	IN	IN
	Advanced Data Manipulation	Normalization	Data normalization function	IN	IN
		Alignment	Retention time alignment function	IN	IN
		Merged Spectrum	Merging spectra function	IN	IN
		Composition	Merging, Subtracting or Dividing objective data	IN	IN
		Sample Merge	Merging sample data	IN	IN
		Msms Spectra Merge	Merging MS/MS spectra function	IN	IN
		Resampling	Resampling spectrum data points	IN	IN
	Advanced Structural Analysis	Glycan Analysis	N-glycan structure assignment with diagnostic ions	IN	IN
		SIMSE	de novo sequencing tool	IN
		Compound Database for SIMSE	Basic compound database for SIMSE	IN	IN
	etc	Clipboard	Clipboard function	IN	IN
		Settings	Environment settings	IN	IN
		Help	Showing helps	IN	IN
		Operation Log	Operation history function	IN	IN
		PluginManager	Plug-in manager	IN	IN
		Edit Sample User Properties	Editing user properties	IN	IN
		Batch Service	Batch operation manager	IN	IN
		Command Line Batch Service	Running specified batch jobs as commands in the background	IN	IN
		Script Plugin	Script Console operation manager	IN	IN
		Iron Python	Iron Python script interpreter	IN	IN
		Simca Display	SIMCA P+ wrapper	IN	IN
		Sample Tree Builder	Building sample tree	IN	IN
Core libraries		CoreFunctions	Fundamental function for C	IN	IN
		CoreToolkits	Fundamental classes for C++	IN	IN
		DataObjects	Basic data object	IN	IN
		DataOperation	Basic data operation	IN	IN
		DbTools	Internal database manager	IN	IN
		EventManager	Event management	IN	IN
		GLTools	3-D graphic management	IN	IN
		IdentificationTools	Identification/quantification manager	IN	IN
		ImageManager	Drawing/imaging manager	IN	IN
		JavaTools	Java-code management library	IN	IN
		NetworkTools	Network access function	IN	IN
		NumericalTools	Numerical calculation function	IN	IN
		PluginTools	Plug-in operation manager	IN	IN
		WindowManager	Graphic User Interface library	IN	IN
		XMLTools	XML file manager	IN	IN
		CLRManager	.NET Framework wrapper (Basic function)	IN	IN
		CLRPluginTools	.NET Framework wrapper (plug-in manager)	IN	IN
ExecutableFile		mspp		IN	IN
		msppcmd		IN	IN
Sample Data	data	-	Sample data	IN	IN(partially)
Independent Package	Identification	PTM Librarian	PTM Librarian wrapper	other package
	development tool kit	-	Library files for C/C++	IN
		-	Include files for C/C++	IN
		-	Setting files of VS wizard for C/C++	IN
		-	Install files of VS wizard for C/C++	IN
		-	VS wizard files for C#	IN
		-	Sample project files	IN