Computational protocol: Comparative systems biology of human and mouse as a tool to guide the modeling of human placental pathology

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Protocol publication

[…] Raw files were converted to m/zXML using ReAdW and searched by X!Tandem against a mouse (v3.28) or human (v3.28) IPI ( protein sequence database. Searches were performed against a target-decoy sequence database and the FDR was set to a conservative level of 0.5% on the peptide level (). Only fully tryptic peptides ⩾7 amino acids, matching these criteria were accepted to generate the final list of identified proteins. We only accepted proteins identified either with two unique peptides or one unique, unambiguous peptide found in ⩾2 MudPIT runs per analyzed organelle fraction. To minimize protein inference, we developed a database grouping scheme and only report proteins with substantial peptide information, as recently reported (; ) (see for details). [...] Comparison of our labyrinth proteome resource to our recently published proteomic data were achieved using the ProteinCenter bioinformatics software (Proxeon Biosystems, Odense, Denmark). To link these datasets, we loaded the accession keys for each of the three projects into ProteinCenter and BLASTed them against each other. Only proteins with at least 95% sequence homology were considered identical. [...] Identified proteins (IPI accessions) and Affymetrix probe annotations were linked to Ensemble gene IDs using the Biomart tool ( and parsed into a MySQL database and linked on the database level (see for details). […]

Pipeline specifications

Software tools ProteinCenter, BioMart
Applications Miscellaneous, Genome annotation
Organisms Mus musculus, Homo sapiens
Diseases Pre-Eclampsia, Genetic Diseases, Inborn