Prosit-Derived Spectral Libraries for Scaffold DIA Searches

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 the same as other 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 - 15,896 entries

Caenorhabditis elegans
Download Caenorhabditis elegans DLIB
Download FASTA file - 4,089 entries

Danio rerio
Download Danio rerio DLIB
Download FASTA file - 3,125 entries

Drosophila melanogaster
Download Drosophila melanogaster DLIB
Download FASTA file - 3,586 entries

Escherichia coli (strain K-12)
Download Escherichia coli DLIB
Download FASTA file - 4,518 entries

Homo sapiens
Download Homo sapiens DLIB
Download FASTA file - 20,350 entries

Mus musculus
Download Mus musculus DLIB
Download FASTA file - 17,025 entries

Rattus norvegicus
Download Rattus norvegius DLIB
Download FASTA file - 8,072 entries

Saccharomyces cerevisiae
Download Saccharomyces cerevisiae DLIB
Download FASTA file - 6,721 entries

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