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Table 1 Comparison of lipid identification software

From: LipidMatch: an automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data

 

LipidMatch

MS-DIAL

GREAZY

LipidSearch 4.1

Identification (ID) Strategy*

Rules

Similarity

Similarity

Rules & Similarity

Fragment Intensity for ID*

Yes (ranking)

Yes

No

Yes

in-silico Library (Types)

56

34

24

59

User Developed Libraries

Yes

Difficult

Difficult

Difficult

Programming Language

R

C#

C++

Java

Restrictions

None

None

None

Purchase License

Multiple Vendor Formats

Yes (.ms2)

Yes (.abf)

Yes (.mzML)

Yes (vendor DLL)

Data Independent Analysis**

Yes

Yes

No

No

MS3 analysis

No

No

No

Yes

Multiple Hits in Final Report

Yes (ranked)

No

No

Yes (ranked)

Structural Resolution***

Correct

Over Reports

Over Reports

Correct

Identifiers (eg. LipidMaps)

No

Yes

No

No

Computational time (HR data)

Slow

Medium

Fast

Fast

Employs False Discovery

No

No

Yes

No

  1. Note that in determining total types of lipids contained in each software’s in silico library all ether linked lipids contained were considered two types (plasmenyl and plasmanyl) and all oxidized lipids contained across numerous classes were considered one lipid type
  2. *Please read text for further information
  3. **Not discussed in-depth in this manuscript. LipidMatch can be applied to AIF data independent analysis (currently only supports Thermo files), while MS-DIAL can be applied to AIF and SWATH approaches
  4. ***Correct reporting of structural resolution means that lipids are annotated only at the level of structure known based on fragmentation