The MTDB Creator can create a standalone Accurate Mass and Time Tag Database (AMT tag DB) compatible with MultiAlign or VIPER. The database is assembled using peptide identifications (identified PSMs) from MS-GF+, X!Tandem, SEQUEST, or MSAlign. It loads the PSMs, align the peptides across datasets, then writes the results to the database.
MTDB Creator can directly load the .mzid files created by MS-GF+. It can also load .mzid.gz files. To process X!Tandem results, .xml file created by X!Tandem must first be converted to a tab-delimited format using the Peptide Hit Results Processor application (PHRP); see GitHub
Start the MTDB Creator, then click "New Analysis Job".
- Click "Add", select "MZIdentML", and select one or more .mzid or .mzid.gz files.
- Alternatively, use "Add Folder" and select a directory with several .mzid or .mzid.gz files.
For X!Tandem, SEQUEST, or MSAlign results, use "Add" then "Old Analysis Files".
- For X!Tandem, select the _xt.txt files created by PHRP.
- For SEQUEST, select the _syn.txt files created by PHRP.
- For MSAlign select _msalign_syn.txt files created by PHRP.
Next, click Options, review the filtering and alignment options, and confirm the database format.
- Click "OK, and the program will prompt you to define the output file path.
It will next load the peptide identifications for each dataset, filter them, and align them against a predicted normalized elution time (NET) scale.
- Once the processing finishes, the AMT tag database will be created, and a window appear with alignment plots.
Example data files are available in a 130 MB .zip file on GitHub named MTDB_Creator_Example_Data.zip for you to explore MTDB Creator's functionality. Unzip that .Zip file to obtain these files:
- MSGF+ results files to be used as input files for MTDB Creator
- QC_Shew_17-02_a_QEP_03Aug18_Wally_18-07-04_msgfplus.mzid.gz
- QC_Shew_17-02_b_QEP_03Aug18_Wally_18-07-04_msgfplus.mzid.gz
- QC_Shew_17-02_d_QEP_25July18_Wally_18-07-04_msgfplus.mzid.gz
- VIPER compatible AMT tag DB created by MTDB Creator
- QC_Shew.mdb
- MultiAlign compatible AMT tag DB created by MTDB Creator
- QC_Shew.mtdb
- Deisotoped features files generated by DeconTools
- See the _isos.csv and _scans.csv files in DeconTools_Results
- MSFileInfoScanner graphics files
The QC_Shew datasets were generated from the analysis of a Shewanella Oneidensis MR-1 QA sample, using a Thermo Q-Exactive Plus mass spectrometer.
Written by Matthew Monroe, Brian LaMarche, Michael Degan, and Bryson Gibbons for the Department of Energy (PNNL, Richland, WA)
E-mail: matthew.monroe@pnnl.gov or proteomics@pnnl.gov
Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://panomics.pnnl.gov/ or https://www.pnnl.gov/integrative-omics
The MTDB Creator 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