Mass Spec Protein Reference

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:

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

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:

Presently, the pipeline is geared towards deuterostomes and vertebrates. Other large divisions coming soon.
A maximum of 500K sequences can be submitted.
The maximum file size that can be submitted is 500 MB.
DO NOT SUBMIT RNA-seq reads. RNA-Seq data must already be assembled using a tool like Trinity.
All sequence identifiers must be unique; otherwise the cluster and assembly phase will fail.
Please submit your mRNA transcripts as cDNA, i.e in DNA not RNA alphabet
Presently, some options are given (cluster % ID, cluster overlap len, assembly % ID). More will be offered in the near future.

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]' )