This program merges the contents of a tab-delimited peptide hit results file from PHRP (for MS-GF+, MaxQuant, X!Tandem, etc.) with the corresponding MASIC results files, appending the relevant MASIC stats to each peptide hit result, writing the merged data to a new tab-delimited text file.
It also supports TSV files, e.g. as created by the MzidToTsvConverter
If the input directory includes a MASIC _ReporterIons.txt file, the reporter ion intensities will also be included in the new text file.
MASICResultsMerger is a console application, and must be run from the Windows command prompt.
MASICResultsMerger.exe
InputFilePathSpec
[/M:MASICResultsDirectoryPath] [/O:OutputDirectoryPath]
[/N:ScanNumberColumn] [/C] [/Mage] [/Append]
[/DartID]
[/S:[MaxLevel]] [/A:AlternateOutputDirectoryPath] [/R]
[/Trace]
The input file should be a tab-delimited file where one column has scan numbers.
By default, this program assumes the second column has scan number, but the /N
switch can be used to change this (see below).
Common input files are
- Peptide Hit Results Processor (https://github.com/PNNL-Comp-Mass-Spec/PHRP) tab-delimited files
- MS-GF+ syn/fht file (
_msgfplus_syn.txtor_msgfplus_fht.txt) - SEQUEST Synopsis or First-Hits file (
_syn.txtor_fht.txt) - X!Tandem
_xt.txtfile
- MS-GF+ syn/fht file (
- MzidToTSVConverter (https://github.com/PNNL-Comp-Mass-Spec/Mzid-To-Tsv-Converter) .TSV files
- This is a tab-delimited text file created from a
.mzidfile (e.g. from MS-GF+)
- This is a tab-delimited text file created from a
If the MASIC result files are not in the same directory as the input file, use /M
to define the path to the correct directory.
The output directory switch is optional. If omitted, the output file will be created in the same directory as the input file.
Use /N to change the column number that contains scan number in the input file.
The default is 2 (meaning /N:2).
When reading data with _ReporterIons.txt files, you can use /C to specify that a
separate output file be created for each collision mode type in the input file
(typically pqd, cid, and etd).
Use /Mage to specify that the input file is a results file from Mage Extractor.
This file will contain results from several analysis jobs; the first column in
this file must be Job and the remaining columns must be the standard Synopsis or
First-Hits columns supported by PHRPReader. In addition, the input directory must
have a file named InputFile_metadata.txt (this file will have been auto-created
by Mage Extractor).
Use /Append to merge results from multiple datasets together as a single file;
this is only applicable when the InputFilePathSpec includes a * wildcard and
multiple files are matched. The merged results file will have DatasetID values of
1, 2, 3, etc. along with a second file mapping DatasetID to Dataset Name.
Use /DartID to only list each peptide once per scan. The Protein column will list
the first protein, while the Proteins column will be a comma separated list of
all of the proteins. This format is compatible with DART-ID
(https://pubmed.ncbi.nlm.nih.gov/31260443/)
Use /S to process all valid files in the input directory and subdirectories.
Include a number after /S (like /S:2) to limit the level of subdirectories to examine.
When using /S, you can redirect the output of the results using /A to specify an alternate output directory.
When using /S, you can use /R to re-create the input directory hierarchy in the alternate output directory (if defined).
Use /Trace to show additional debug messages while searching for input files
Written by Matthew Monroe for the Department of Energy (PNNL, Richland, WA)
E-mail: [email protected] or [email protected]
Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://www.pnnl.gov/integrative-omics
Source code: https://github.com/PNNL-Comp-Mass-Spec/MASIC-Results-Merger
MASICResultsMerger is licensed under the Apache License, Version 2.0; you may not use this file except in compliance with the License. You may obtain a copy of the License at https://opensource.org/licenses/Apache-2.0