This is a companion site to the paper Curr Biol. 2014 Jul 7;24(13):1467-75
Deep Proteomics of the Xenopus laevis egg using an mRNA-derived Reference Database
by Wühr M, Freeman RM Jr, Presler M, Horb ME, Peshkin L, Gygi SP, Kirschner MW.

Downloadable files: Final protein reference database
Gene Symbols PHROG_1r0 Gene Symbol assignment for PHROG
Spectra_Pep_Prot_Mapping.xlsx Peptide/protein mapping of MS spectra Scripts to locally run your own installation of the pipeline (the same scripts used to create PHROG) + short How-To document
XGI.shuff.small.fa If you don't have an mRNA transcript file to test our pipeline - download this sample file and use it in the form below.
mmc2.xlsx Document S2. Tables S4-S6. Estimated Protein Concentrations for Approximately 11,000 Proteins in the X. laevis Egg

Creating a protein reference

This web tool makes a protein reference database from mRNA transcripts (in cDNA form) that is highly optimized for mass spec searches. To create your own protein reference database, plesae fill in the details below. Please remember the following:

Upload your FASTA file of mRNA (cDNA) transcripts...

Cluster/Assembly Options:

Clustering % identity
Cluster minimum overlap length (bp)
Assembly % identity

Translation frame/frameshift detection:
BLASTX detection database
Translation filter E cutoff

Please give us your e-mail address to which we can send the results:


If you should encounter any errors while submitting a job or during job processing, please contact Leon Peshkin or Bob Freeman. Please be patient -- support requests will be handled has quickly as possible.

Other tools...

Gene symbol assignment to proteins

New versatile gene symbol assignment to proteins

An AWK script to digest proteins into Tryptic peptides ( Trypsin is '[KR][^P]' )