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 PTMs for Prosit other than oxidation.
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. If they vary dramatically from your settings please contact us.
Parameter | Setting |
Charge Range | 2 - 3 |
Maximum Missed Cleavages | 1 |
m/z Range | 396.4 - 1002.7 |
Default NCE | 33 |
Default Charge | 3 |
Featured Libraries
Coronavirus reference
Download Coronavirus only DLIB
Download Coronavirus plus Human (pan human) DLIB
Download Coronavirus only FASTA - 13 entries
Download Coronavirus plus Human FASTA - 20,350 entries
Available Libraries
Arabidopsis thaliana
Download Arabidopsis thaliana DLIB
Download FASTA file accessed 10/22/19 - 15,896 entries
Caenorhabditis elegans
Download Caenorhabditis elegans DLIB
Download FASTA file accessed 10/23/19 - 4,089 entries
Danio rerio
Download Danio rerio DLIB
Download FASTA file accessed 10/22/19 - 3,125 entries
Drosophila melanogaster
Download Drosophila melanogaster DLIB
Download FASTA file accessed 10/22/19 - 3,586 entries
Escherichia coli (strain K-12)
Download Escherichia coli DLIB
Download FASTA file accessed 10/22/19 - 4,518 entries
Homo sapiens
Download Homo sapiens DLIB
Download FASTA file accessed 10/22/19 - 20,350 entries
Mus musculus
Download Mus musculus DLIB
Download FASTA file accessed 10/22/19 - 17,025 entries
Rattus norvegicus
Download Rattus norvegius DLIB
Download FASTA file accessed 10/22/19 - 8,072 entries
Saccharomyces cerevisiae
Download Saccharomyces cerevisiae DLIB
Download FASTA file accessed 10/22/19 - 6,721 entries
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