### 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](http://www.ncbi.nlm.nih.gov/pubmed/24392666). ### License PeptideEclipse is licensed under a Creative Commons Attribution 3.0 Unported License.
ulo/PeptideEclipse
Map your peptide identifications to transmembrane regions as annotated in UniProt.
Java