GEN-MKT-18-7897-A
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While generating proteomic spectral libraries today is relatively easy, sometimes a library is needed and there is not time or need to generate a deep library using the traditional data-dependent acquisition approach. Here, a strategy will be outlined to generate a data-independent acquisition (DIA) spectral library from a FASTA file using DIA-NN software for use with a SCIEX QTOF system. For the most up-to-date information on the use of DIA-NN software and more detailed instructions, please see the DIA-NN software documentation. Download the latest version of DIA-NN software from GitHub.
The first step is to obtain a FASTA file for your organism of interest, from a source such as the UniProt website, shown below. On this website, you can filter by organism to download a FASTA file of interest in either the canonical or the canonical+isoform format.
Then, the DIA-NN software is used to build a spectral library from the FASTA file. No datafiles are needed for this step, as the software will generate a library in silico for the proteins and peptides included in the FASTA file. More details for creating libraries from FASTA files can be found in the library-free instructions in the DIA-NN software documentation.
The dialogue box, below, shows recommended settings for building a library in the DIA-NN software.
It could take up to 1–2 hours to generate the library, depending on its size.
Once created, you can use the generated *.speclib file as you would use any other library to process your SWATH DIA data with DIA-NN.
RUO-MKT-18-14611-A
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