PeptideEclipse

Welcome to PeptideEclipse

PeptideEclipse allows you to map your proteomics peptide identifications to transmembrane regions as annotated in UniProt, and thus showing which peptides were completely or partially hidden within the lipid bilayer.

Homepage: http://ulo.github.io/PeptideEclipse/

Input

First, download the corresponding UniProt Knowledgebase packages from their FTP server:

ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/

Note: you do not have to unzip the files!

Then just provide the ProteinProphet output, either the complete prot.xml file or a filtered and exported prot.xls file.

Command

To run PeptideEclipse type the following into your command line:

java -jar PeptideEclipse.jar -in inFile -up uniprot1.dat.gz [uniprot2.dat.gz ...] > outFile

• inFile: a ProteinProphet file (e.g: interact.prot.xml | interact.prot.xls)
• outFile: target file (e.g: interact.prot.tmAnalysis.tsv)

Output

For a prot.xml file input, PeptideEclipse will generate a tab-separated file (open using Excel) with the following columns:

group_number    protein-group number
group_probability   protein-group probability
protein_name    name of first protein
protein_peptides    number of peptides
protein_pct_spectrum_ids    percent of total spectral counts
protein_percent_coverage    percent of protein sequence coverage
peptide_sequence    stripped peptide sequence
peptide_sequence_modified   modified peptide sequence
peptide_charge  peptide charge state
peptide_nsp_adjusted_probability    peptide probability
peptide_n_enzymatic_termini number of proteolytic termini
peptide_calc_neutral_pep_mass   neutral theoretical peptide mass
proteinID   matching UniProt ID
protein_transmemRegions UniProt transmembrane domain count
protein_AA  length of protein
protein_AA_covered  length of protein covered by peptides
protein_AA_transmem length of protein's TM region(s)
protein_AA_transmem_covered length of protein's TM region(s) covered by peptides
peptide_AA  length of peptide
peptide_AA_transmem length of peptide's TM region(s)

For a prot.xls file input, PeptideEclipse will create a copy of the input file with the following columns appended:

peptide_AA  length of peptide
peptide_AA_transmem length of peptide's TM region(s)
proteinID   matching UniProt ID
protein_transmemRegions UniProt transmembrane domain count
protein_AA  length of protein
protein_AA_covered  length of protein covered by peptides
protein_AA_transmem length of protein's TM region(s)
protein_AA_transmem_covered length of protein's TM region(s) covered by peptides

Dependencies

All dependencies are packed within the PeptideEclipse.jar file. No external dependencies are needed! Internally, PeptideEclipse depends on two libraries:

• Apache Commons CLI: http://commons.apache.org/proper/commons-cli/
• Google Guava: http://code.google.com/p/guava-libraries/

Credits

PeptideEclipse was developed by Ulrich Omasits, and was published as part of a proteomics study. Please cite Waas et al. Anal Chem. 2014 Feb 4;86(3):1551-9.

License

PeptideEclipse is licensed under a Creative Commons Attribution 3.0 Unported License.