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LaCyTools is open-source software for researcher focussing on chromatography coupled to mass spectrometry. It includes modules for retention time and m/z calibration, peak integration, quality control and more. The tool was first described in a 2016 Journal of Proteome Research article, located at <https://pubs.acs.org/doi/10.1021/acs.jproteome.6b00171>
The CPM fork of LaCyTools contains a small number of fixes and changes. Details can be found in the Git history.
* Updated `README.md`
* Updated `LaCyTools.py`
The original location of LaCyTools is: <https://github.com/Tarskin/LaCyTools>
LacyTools requires Python 3 and several additional packages. To install Python 3 on Windows, download and install Python from https://www.python.org/ftp/python/3.12.7/python-3.12.7-amd64.exe. **Make sure to select ```Add python.exe to PATH``` during installation**. On recent Linux distributions, Python 3 is part of the standard installation.
To install the additional packages, on the command prompt (on Windows, hit the "windows key" and type ```CMD```), execute:
pip3 install --user scipy matplotlib numpy tables
```
To install for all users, execute the "command prompt" as administrator (right click "run as administrator"), and omit the "--user" part of the install command above.
Download the latest LaCyTools from:
Extract the zip file in the location where you want to run LacyTools.
Start LacyTools by double clicking on the file ```LaCyTools.bat``` (Windows Batch File), **NOT** ```LaCyTools.py``` .
See the file LICENSE.txt for information on the history of this software, terms & conditions for usage, and a DISCLAIMER OF ALL WARRANTIES.
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## Files
LaCyTools uses several input files, some of which must be manually created. The input files are described below.
### *.mzxML
The primary input are mzXML files with profile (non peak picked) MS1 spectra.
The main aim of LaCyTools is to determine the relative abundance (peak content) of selected compounds.
Retention times, masses, and other properties of the compounds of interest are set in other input files described below.
Before the compounds are quantified, the mzXML files are aligned, and the m/z values are calibrated. Retention time alignment is done using the file alignment.txt (see below), while m/z calibration is done using the file reference.txt (see below).
### settings.txt
The file settings.txt contains general settings used by LaCyTools. It can be generated through menu item "Settings -> Settings".
### alignment.txt
The first step in processing the mzXML files is alignment of the retention times. For this, LaCyTools uses the file alignment.txt.
This file contains the retention times of peaks that are present in all mzXML files.
The file is TAB separated, and must be manually created (in text editor or Excel). The following example shows its format:
|m/z |Seconds |
|------------|--------|
|878.6868 |51 |
|932.7044 |51 |
|1029.7362 |51 |
|1083.7538 |51 |
|873.3552 |92 |
|927.3728 |92 |
|1024.4046 |92 |
|1078.4222 |92 |
|868.0235 |140 |
|922.0412 |140 |
|1019.073 |140 |
|1073.0906 |140 |
### reference.txt
The file reference.txt contains the list of compounds that are to be quantified.
The file is TAB separated, and must be manually created (in text editor or Excel). The following example shows its format:
|# Peak | RT | Mass Window |Time Window | Min Charge |Max | Calibrant |
|----------------|------|-------------|------------|------------|----|-----------|
| IgGI1H3N4F1 | 59.6 | 4 | | | | |
| IgGI1H4N4F1 | 59.6 | 4 | | | | x |
| IgGI1H4N4F1S1 | 59.6 | 4 | | | | x |
| IgGI1H5N4F1S1 | 59.6 | 4 | | | | |
| IgGII1H3N4F1 | 144.4| 4 | | | | |
| IgGII1H4N4F1 | 144.4| 4 | | | | x |
| IgGII1H5N4F1 | 144.4| 4 | | | | x |
| IgGII1H4N5F1 | 144.4| 4 | | | | |
| IgGII1H4N4F1S1 | 144.4| 4 | | | | |
| IgGII1H5N4F1S1 | 144.4| 4 | | | | |
Use the format: ```[pep]1H[w]N[x]F[y]S[z]```. The letters w, x, y and z are the number of sugars present in the glycan structure. For non fucosylated and non sialylated use F0 and S0 respectively.
### analytes.ref
The file analytes.ref contains the retention time interval, and m/z of all isotopes and charges of the compounds of interest.
The file is generated by LaCyTools using ```reference.txt``` as input.
LacyTools does not automatically detect when m/z values of compounds are out of the measured range. This will affect/invalidate
the results of the quantification. Therefore, it is important to check the m/z values in ```analytes.ref```, and adjust the
charge states in ```reference.txt``` if necessary.