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.
|PHROG_1r0.fasta.zip||Final protein reference database|
|Gene Symbols PHROG_1r0||Gene Symbol assignment for PHROG|
|Spectra_Pep_Prot_Mapping.xlsx||Peptide/protein mapping of MS spectra|
|make_mz_ref_db_scripts.zip||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|
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:
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.
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]' )