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TWIMExtract_Help.txt
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TWIMExtract_Help.txt
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********************************************************************************
TWIMExtract User Guide
**IF YOU USE TWIMEXTRACT, PLEASE CITE:**
Haynes, S. E.; Polasky, D. A.; Dixit, S. M.; Majmudar, J. D.; Neeson, K.; Ruotolo, B. T.; Martin, B. R.
"Variable-Velocity Traveling-Wave Ion Mobility Separation Enhancing Peak Capacity for Data-Independent
Acquisition Proteomics". Anal. Chem. 2017, acs.analchem.7b00112.
********************************************************************************
Setup:
1) Download TWIMExtract_Setup.exe from http://sites.lsa.umich.edu/ruotolo/software/twim-extract/
2) Run TWIMExtract_Setup.exe. Setup will create a shortcut (Run_TWIMExtract.bat) that should be used
to run the program.
3) Double click Run_TWIMExtract.bat to run TWIMExtract
General Info/Purpose:
- TWIMExtract will pull data from Waters .raw files using user-defined 'range files'.
- Extracted data will be collapsed to one dimension, saving either chromatographic retention time (RT),
ion mobility drift time (DT), or the mass spectrum (MZ) to one axis and intensity to the other.
- Extracted data are saved to a comma separated text file (.csv) without further processing
Basic Use:
1) To use TWIMExtract, start the program by double clicking the Run_TWIMExtract.bat shortcut
2) Prepare range/rule files:
- To use TWIMExtract, the range(s) of data you want to extract need to be defined
- This can be done with range files or rule files:
- Range files are simple text files with 6 fields denoting the starting and ending
retention time, drift time, and m/z to define a cube in the 3D RT-DT-MZ dataset.
TWIMExtract will collapse all data in the cube onto the desired axis and output a
text file (.csv) with the information.
**See example range file in C:\TWIMExtract\_EXAMPLES for a template**
Example range file:
MZ_start_(m/z): 100
MZ_end_(m/z): 8000
RT_start_(minutes): 0
RT_end_(minutes): 100
DT_start_(bins): 1
DT_end_(bins): 200
- Rule files are created using Driftscope (from Waters). In Driftscope, regions of DT-MZ
space can be selected. To create a rule file, save the selected region using
File\Export Selection Rule. This will create a .rul file that can be selected for
use in TWIMExtract. See 'Making Selection Rules' in the Examples folder
(C:\TWIMExtract\_EXAMPLES) for more info.
3) Select the raw data to extract from using the "Browse Data" button in TWIMExtract
***NOTE: for convenience, the default raw, range, and rule file directories can be set using
the options under the file menu. Then the buttons will open to the chosen directories when pressed. ***
4) Choose your extraction settings. These can be adjusted using the options menu (top) and the check boxes (bottom)
of the extractor interface. The primary options are:
- Range or Rule file mode: whether to use range (.txt) or rule (.rul) files for the extraction
- Combine Raw: 3 options - "ALL", "BY FUNCTN", and "NO". Whether to combine across raw files. If "ALL"
is selected, data from all raw files present in the table will be combined into a single output
csv file. If "BY FUNCTN" is selected, all Functions from a single raw file will be combined into a
single output csv, but separate raw files will each generate their own output csv. If "NO" is selected,
no raw data will be combined and all functions and raw files will get their own output csv.
- Combine Range: "YES" or "NO". If yes, extracted data from all selected range files will be combined into
a single output csv file. If no, each range file will result it a separate output csv file.
NOTE: If combining "ALL" raw files AND ALSO combining across range files, it is possible to use excessive memory
and cause computer problems/crashes if extracting huge amounts of data (1000s of raw/range files).
If extracting large amounts of data, it is strongly recommended not to use this mode.
- Save info: Whether to save any information about the file (collision voltages or IM settings) to the
output file as a header.
- For DT (drift time) extractions, output can be saved in milliseconds (ms) or bins. ms is the default,
but may fail on some instrument types. ***IF MILLISECOND EXTRACTION FAILS, TRY USING BINS***
5) Select the type of extraction (RT, DT, or MZ) using the appropriate button. This will open a filechooser
to select your desired range or rule file(s). Once the files are selected, extraction will begin.
NOTE: extraction may take some time. Typically a few seconds per range file, but can be longer for large raw files.
Advanced/Other modes:
- Batch mode: To run multiple extractions in series, a batch can be generated. Batches consist of a single .csv
file that contains the location of a FOLDER containing raw files in one column and a FOLDER containing
range or rule files in the second column. Each line in the batch .csv represents a single extraction - that is,
all the raw files in the folder from column 1 will be extracted using all the range files from the folder in column 2.
A one line batch .csv file is the same as a single regular extraction using the TWIMExtract interface, but many lines
can be added to create batches of arbitrary size.
- To use batch mode, click the Batch menu at the top of the interface, then 'select batch csv and run batch'. This
will open a file chooser to select the .csv file with batch information. The batch will begin running as soon as
the .csv file is selected.
- For more information, see the batch example in the examples folder.
- Legacy range file mode: If you used the beta version of TWIMExtract and have old format range files (containing 9 fields
instead of 6), those files can still be used by selected 'Legacy range file mode' in the Advanced menu.
- Careful mode: **most users should not have to worry about this**
- If a raw file contains multiple functions to be extracted, the default behavior of TWIMExtract is to use the
same number of bins for each function, since getting bin sizes takes as long as actually extracting the data.
This should not be a problem unless two functions within the same raw file have mass ranges that differ
significantly in size (e.g. function 1 is from 500-1000 m/z and function 2 is from 100-10000 m/z).
In that example, function 2 would have fewer m/z bins than it should, possibly resulting in artifical loss of
resolution.
- Careful mode gets the number of bins individually for each function to avoid resolution losses, but is slower
than normal mode as a result.
- Command line arguments: can be used for scripting with TWIMExtract. NOTE: not all features are available in command line mode.
General use: java -jar TWIMExtract.jar [ARGS]
Help: java -jar TWIMExtract.jar -h
NOTE: directories must be in quotes ("") if they contain spaces or other special characters
Arguments:
Required:
-i "[input directory]" : The full system path to the .raw file from which to extract
-o "[output directory]" : The full system path to the folder in which to save output
-m [mode] : the extraction mode (the dimension of data to save). 0 = RT, 1 = DT, 2 = MZ
Optional:
-f [func] : the individual function to extract. If not provided, extracts all functions
-r "[Range path]" : The full system path to a range (.txt) or rule (.rul) file to use
for extraction. If not provided, extracts the full ranges in all dimensions
-rulemode [true or false] : Whether to use range or rule file.
-combinemode [true or false] : Whether to combine all outputs from a single raw file
(e.g. multiple functions) into a single output.
-ms [true or false]: whether to save DT extractions in milliseconds (ms) or bins.
Example: The command below would extract DT information from all functions from the
"My_data.raw" file using the "my_range.txt" range file, combine the output using bins as the
DT information, and place it in C:\Extracted Data:
java -jar TWIMExtract.jar -i "C:\Data\My_data.raw" -o "C:\Extracted Data" -m 1
-r "C:\Ranges\my_range.txt" -rulemode false -combinemode true -ms false
License information: (BSD)
Copyright 2016 Daniel Polasky
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
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3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS
BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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