Section 4 (lipid identification from untargeted lipidomics datasets – HRAM MS, DDA, DIA)

* NA – not applicable

	MS-DIAL	OzFAD	Skyline	Lipid Data Analyzer (LDA)	LipidFinder	LipidHunter 2	LipidXplorer	Lipostar 2.0	LPPtiger	MZmine	XCMS on-line
Shotgun MS/MS	Yes	Yes	Yes	No	No	Yes	No	No	No	Yes	No
LC-MS(MS)	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
MS2 DDA	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes	No	Yes	No
MS2 DIA	Yes AIF/SWATH	Yes	Yes AIF/SWATH	No	No	No	No	Yes AIF/SWATH	No	No	No
Ion mobility CCS annotation	Yes Yes	No No	Yes Yes	No No	No No	No No	No No	Yes No	No No	No No	No No
Oxidized lipids Oxidized lipid coverage	Yes FA;GL;GP;	No —	Yes —	Yes Oxo-, keto-, epoxy-, furan-, hydroxyl-, epidioxy-, carboxy-, hydroperoxy-, cyclopentane-, bromo-, chloro-, fluoro-, iodo-, and nitro- for 4 out of 8 LIPID MAPS categories	No —	No —	No —	Yes 8 out of 8 LIPID MAPS categories	Yes GP	No —	No —
Spectra matching based ID	Yes	No	No	No	No	No	No	Yes	No	Yes	No
Decision rules based ID	Yes	Yes	No	Yes	No	Yes	Yes	Yes	No	Yes	No
Spectra annotation	Yes	Yes	Yes	Yes	No	Yes	No	Yes	No	Yes	No
Support multiple adducts	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	No	Yes	Yes
Correction for in source fragmentation	No	No	Yes	No	Yes	No	No	Yes	No	No	No
Batch processing	Yes	No	Yes	Yes	Yes	Yes	Yes	Yes	No	Yes	Yes
Input format	MzML, cdf, abf, hive, sciex, waters, bruker, shimadzu, thermo, agilent	Raw data from OzID-modified Synapt G2-Si	Reads Agilent, Bruker, Sciex, Shimadzu, Thermo, Waters, mzXML, mzML, mz5. Imports most search tool outputs.	MzXML, .d(Agilent), .d(Bruker), .wiff(SCIEX), .wiff.scan(SCIEX), .raw(Thermo), .raw(Waters)	CSV, TSV, Excel	MzML	MzML, mzXML, .raw(Thermo)	.d(Agilent), .d(Bruker), Shimadzu, .raw(Thermo), .raw(Waters)	MzML	MzML, imzML, mzXML, mzData, netCDF, .tdf(Bruker), .raw(Thermo), .raw(Waters)	MzXML, mzData, mzData.XML, netCDF, CDF, .wiff(SCIEX), .wiff.scan(SCIEX)
Output formats	Mztab-M, ms-dial format table (txt), massbank, msp, mgf	Csv, xlsx, sky	Iteratively create methods for major mass spec vendors. Custom reports.	TSV, Excel, mzTab-M, rdb	CSV, Excel, PDF	Excel, html	Excel, mzTab	CSV, Excel, Word	Excel, html	CSV, MetaboAnalyst, mzTab, SQL, XML, GNPS, SIRIUS	Excel, PDF, HTML (incl. images)