The freely available LipidBlast EXCEL templates are the backbone of the LipidBlast MS/MS library development. They contain 5-6 million single values, including the metadata such as formula, accurate mass and name as well as the fragments and accurate masses for each precursor ion, their associated adduct form and all subsequent product ions. The template is coded in MS EXCEL with and additional Visual Basic Macro component. Using a single mouse click around 57 single MS/MS libraries are created in around 1.5 minutes. These ASCII files can then be converted into NIST MS/MS libraries using Lib2NIST and imported into different softwares or used in other independent library search products.
The LipidBlast templates are treasure trove for researchers that want to investigate the fragmentations, neutral losses, specific compound fragments and adduct masses in negative and positive mode. The EXCEL AutoFilter gives easy access to very specific side chains, neutral losses and fragment masses for validation. For each of the lipid classes a single sheet exists, different adducts of the same lipid class are contained in the same sheet. The peak abundances are (unfortunately) hard coded into the EXCEL VBA (Visual Basic) code, but a custom export sheet exists, which allows for easy adjustment of fragment masses and their abundances.
What are some of the associated problems?
Structural diversity is a big issue, because many of the fatty side chains range from C2 to C26 for the major glycerophospholipids or only C14 to C26 for cardiolipins. That means the structural lipid space is in some cases too large and in some cases too small. For example odd carbon number fatty acids C15 or C17 can be found in humans, even they are low abundant. Odd carbon number fatty acyls are very often found in plants, algae and bacteria. Very long chain polyunsaturated fatty acids (VLC PUFA) with fatty acyls up to C40 can be found in the retina or spermatozoa. The current release of LipidBlast does not account for VLCPUFAs simply because of the sheer size of spectra, however VLC PUFA libraries can be created very easily with the provided templates. Generalized text book dogmas regarding biochemistry also change quickly with novel and more sensitive detection methods. The stereochemistry and regioisomerism of the included compounds is another issue. LipidBlast includes stereochemistry information for a few compound classes, mainly those derived from LipidMaps. However MS/MS spectra without physical compound separation (via chromatography) are often not sufficient for stereoisomer differentiation. For example FA 18:2 is included with five different isomer structures 18:2(6Z,9Z); (9E,10E); (9E,12E); (9Z,11Z); (9Z,12Z). Additionally these isomers mostly cover mammalian lipids, the structural diversity of fatty acyls in algae and bacteria is even larger. Instead of the most common 25 acyl chains, an array of more than 230 fatty acyl building blocks have been reported in the literature for algal and bacterial fatty acyls. These do not even include substituted such as -methyl or oxidized fatty acyls. The result is that during compound matching multiple equivalent results are obtained (because they are isobars plus they have the same MS/MS fragments). The solution is to disregard stereochemistry and only export single unique spectra or built taxonomy specific libraries. The free availability of the EXCEL templates allow for flexible solutions to many of the mentioned problems.
What is an MSP file?
The EXCEL templates directly export MSP files. These MSP files are ASCII text files and contain the name, short name, adduct type, accurate isotopic masses as well as the precursor ion, all product ions and most importantly the annotations for all the ions.
There is a certain redundancy included due to backward compatibility to older LIB2NIST versions. The MSP files can be imported into any MS/MS search software. The easiest way is to convert them to NIST MS libraries and use NIST MS Search and NIST MS PepSearch to perform compound annotations. In order to change the format of the MSP files the associated VBA code must be changed. It also contains a function to export unique fragment masses, therefore additional unique product ion mass *.MSP.MSP files are created.
LINKS and downloads
- LIB2NIST the MS/MS library converter [LINK]
- Fatty acids at LipidLibrary [LINK]
- The freely available LipidBlast templates - see download section [LINK]