Prosit is a deep learning algorithm developed by the Wilhelm and Kuster group to predict fragmentation and retention times for peptides. We use Prosit to predict DIA-specific libraries from all possible +2H and +3H peptides in FASTA databases. While the search time is roughly the same as FASTA searches, Scaffold DIA is specifically designed to perform proteome-scale searches, such that Prosit libraries perform as well as smaller sample or tissue-specific DDA libraries used by other tools without the need to perform any DDA library-generation experiments. This approach is particularly powerful when combined with the chromatogram library method to calibrate Prosit libraries for each sample type and instrument.
Proteome Software has built a repository of spectral libraries for common organisms which are available below. If you would like us to make a specific Prosit library for you, please contact us with an organism-specific FASTA (with only reviewed entries). Please note that Prosit will only work with carbamidomethylated peptides (C+57). You cannot use any other cysteine alkylation method and you cannot add any modifications.
See this paper for more information.
Library Creation Parameters
The following parameters were used in the conversion process and thus should match your instrumentation settings. Note, for best results it is important that your library is generated with the correct normalized collision energy (NCE) setting. See this article for more information. If settings vary from your configuration, please contact us.
|Charge Range||2 - 3|
|Maximum Missed Cleavages||1|
|m/z Range||396.4 - 1002.7|
Download Coronavirus only DLIB (1.9 MB)
Download Coronavirus plus Human (pan human) DLIB (259 MB)
Download Coronavirus only FASTA - 13 entries
Download Coronavirus plus Human FASTA - 20,350 entries
Download Arabidopsis thaliana DLIB (1.2 GB)
Download FASTA file accessed 10/22/19 - 15,896 entries
Download Caenorhabditis elegans DLIB (380 MB)
Download FASTA file accessed 10/23/19 - 4,089 entries
Download Danio rerio DLIB (250 MB)
Download FASTA file accessed 10/22/19 - 3,125 entries
Download Drosophila melanogaster DLIB (365 MB)
Download FASTA file accessed 10/22/19 - 3,586 entries
Escherichia coli (strain K-12)
Download Escherichia coli DLIB (222 MB)
Download FASTA file accessed 10/22/19 - 4,518 entries
Download Homo sapiens DLIB (1.9 GB)
Download FASTA file accessed 10/22/19 - 20,350 entries
Download Mus musculus DLIB (1.6 GB)
Download FASTA file accessed 10/22/19 - 17,025 entries
Download Rattus norvegius DLIB (682 MB)
Download FASTA file accessed 10/22/19 - 8,072 entries
Download Saccharomyces cerevisiae DLIB (512 MB)
Download FASTA file accessed 10/22/19 - 6,721 entries