The Protein Coverage Summarizer can be used to determine the percent of the residues in each protein sequence that have been identified.
The program requires two input files:
- a file with protein names and protein sequences (optionally with protein description). This can be a tab-delimited text file or a FASTA file
- a file with peptide sequences and optionally also protein names for each peptide
A graphical user interface (GUI) is provided to allow the user to select the input files, set the options, and browse the coverage results. The results browser displays the protein sequences, highlighting the residues that were present in the peptide input file, and providing sequence coverage stats for each protein.
Download a .zip file with the installer from: https://github.com/PNNL-Comp-Mass-Spec/protein-coverage-summarizer/releases
The release page also includes a .zip file with PeptideToProteinMapper.exe
Input files:
- BSA_P171_QID1638_TestPeptides.txt
- BSA_P171_QID1638_TestPeptides_SequenceOnly.txt
- BSA_P171_QID1638_TestProteins.fasta
Output files:
- BSA_P171_QID1638_TestPeptides_coverage.txt
- BSA_P171_QID1638_TestPeptides_ProteinToPeptideMapping.txt
- BSA_P171_QID1638_TestPeptides_SequenceOnly_coverage.txt
- BSA_P171_QID1638_TestPeptides_SequenceOnly_ProteinToPeptideMapping.txt
There are two options for computing protein coverage and peptide to protein mapping from the command line:
- ProteinCoverageSummarizerGUI.exe
- PeptideToProteinMapper.exe
ProteinCoverageSummarizerGUI.exe
/I:PeptideInputFilePath /R:ProteinInputFilePath [/O:OutputDirectoryName]
[/P:ParameterFilePath] [/F:FileFormatCode] [/SkipHeader]
[/G] [/H] [/M] [/K] [/D] [/Debug] [/KeepDB]
The input file path can contain the wildcard character *. If a wildcard is present, the same protein input file path will be used for each of the peptide input files matched. If the input file has one column of data, it is assumed to be Peptide Sequence. If two columns of data (separated by a tab character), it is assumed to be Protein Name then Peptide Sequence.
The output directory name is optional. If omitted, the output files will be created in the same directory as the input file. If included, a subdirectory is created with the name OutputDirectoryName.
The parameter file path is optional. If included, it should point to a valid XML parameter file.
Use /F to specify the peptide input file format code. Options are:
| Format Code | Type | Comment |
|---|---|---|
| 0 | Peptide sequence in the 1st column | Subsequent columns are ignored |
| 1 | Protein name in 1st column and peptide sequence 2nd column | |
| 2 | Generic tab-delimited text file | Will look for a column titled 'Peptide'; also looks for Protein and Scan, though these are not required |
Use /SkipHeader to skip the first line when the file format is Sequence Only or Protein Name and Sequence
Use /G to ignore I/L differences when finding peptides in proteins or computing coverage.
Use /H to suppress (hide) the protein sequence in the _coverage.txt file.
Use /M to enable the creation of a protein to peptide mapping file.
Use /K to skip protein coverage computation steps
Use /D to duplicate the input file, creating a new file with one line per peptide/protein combo
Use /Debug to keep the console open to see additional debug messages
Use /KeepDB to keep the SQLite database after processing (by default it is deleted)
The PeptideToProteinMapper reads in a text file containing peptide sequences then searches the specified .fasta or text file containing protein names and sequences to find the proteins that contain each peptide. The program will also compute the sequence coverage percent for each protein (though this can be disable using /K).
PeptideToProteinMapper.exe
/I:PeptideInputFilePath /R:ProteinInputFilePath
[/O:OutputDirectoryName] [/P:ParameterFilePath] [/F:FileFormatCode]
[/N:InspectParameterFilePath] [/G] [/H] [/K] [/A]
[/L[:LogFilePath]] [/LogDir:LogDirectoryPath] [/VerboseLog] [/Q]
The input file path can contain the wildcard character *. If a wildcard is present, the same protein input file path will be used for each of the peptide input files matched.
The output directory name is optional. If omitted, the output files will be created in the same directory as the input file. If included, then a subdirectory is created with the name OutputDirectoryName.
The parameter file path is optional. If included, it should point to a valid XML parameter file.
Use /F to specify the peptide input file format code. Options are:
| Format Code | Type | Comment |
|---|---|---|
| 0 | Auto Determine | Treated as /F:1 unless name ends in _inspect.txt, then /F:3 |
| 1 | Peptide sequence in the 1st column | Subsequent columns are ignored |
| 2 | Protein name in 1st column and peptide sequence 2nd column | |
| 3 | Inspect search results file | Peptide sequence in the 3rd column |
| 4 | MS-GF+ search results file | Peptide sequence in the column titled 'Peptide'; optionally scan number in the column titled 'Scan' |
| 5 | Peptide Hit Results Processor (PHRP) file | PHRP creates tab-delimited text files for MS-GF+, X!Tandem, SEQUEST, or Inspect results |
| 6 | Generic tab-delimited text file | Will look for a column titled 'Peptide'; also looks for Protein and Scan, though these are not required |
When processing an Inspect search results file, use /N to specify the Inspect
parameter file used (required for determining the mod names embedded in the
identified peptides).
Use /G to ignore I/L differences when finding peptides in proteins or computing coverage
Use /H to suppress (hide) the protein sequence in the _coverage.txt file
Use /K to skip the protein coverage computation steps (enabling faster processing)
Use /A to create the _AllProteins.txt file, listing each of the peptides in the input file,
plus one line per mapped protein for that peptide
Use /L to create a log file, optionally specifying the file name
Use /LogDir to define the directory in which the log file should be created
Use /VerboseLog to create a detailed log file
Written by Matthew Monroe and Nik�a Blonder for the Department of Energy (PNNL, Richland, WA) in 2005
E-mail: matthew.monroe@pnnl.gov or proteomics@pnnl.gov
Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://www.pnnl.gov/integrative-omics
The Protein Coverage Summarizer is licensed under the 2-Clause BSD License; you may not use this program except in compliance with the License. You may obtain a copy of the License at https://opensource.org/licenses/BSD-2-Clause
Copyright 2018 Battelle Memorial Institute