I use ThermoFisher .raw files to explore materials that absorb UV light, and I use a specific program called XCalibur Qual Browser. I called ThermoFisher Customer support and they said that there is no in-house computer language that can be used to automate data processing of these .raw files. I was wondering if someone here might know of a Python library or some other computer language that can be used to data process these .raw files. In the photo provided, the top panel shows what materials are, and the bottom panel shows the light-absorbing properties of the materials. I am trying to make the computer language data process the bottom panel of data, not the top one.
Hi, can you share a sample .raw file. I can experiment with it via python or c++ Diego Calderon-Arrieta
Use the `pyopenms` library, which provides an interface to handle mass spectrometry data, including .raw files. Here's an example of how you can use `pyopenms` to access and process the data:
1. Install the `pyopenms` library using pip:
```bash
pip install pyopenms
```
2. Import the necessary modules in your Python script:
```python
import pyopenms
```
3. Load the .raw file using `pyopenms.MSDataFile`:
```python
filename = "path/to/your/file.raw"
ms_data = pyopenms.MSDataFile(filename)
```
4. Access the spectra data from the .raw file:
```python
spectra = ms_data.getSpectra()
```
5. Iterate over the spectra and extract the desired information:
```python
for spectrum in spectra:
# Process the spectrum data, such as extracting intensity values or m/z ratios
# based on your specific needs
pass
```
With the `pyopenms` library, you can access the spectral data stored in the .raw files and perform various processing tasks, such as extracting intensity values, m/z ratios, or other properties of interest from the bottom panel of data you mentioned
Apart from `pyopenms`, there are other Python libraries available for mass spectrometry data analysis, such as `mzML`, `pyteomics`, and `ms_peak_picker`. You can explore these libraries as well if they better suit your requirements.
Good luck
Good afternoon Danial Sh. and Mohammad Imam -
Thank you very much for sharing your time and energy to look into my question. I will try and respond to your comments within 1-2 weeks.
I hope both of you have a delightful two weeks!
Danial Sh. I am very sorry for this long absence. Here is a dropbox link to the .raw file that is similar to the photo.
https://www.dropbox.com/scl/fi/9dltnh1r73ja3pe02xtkd/BG_bulk_PO_x1_conc_1_96_mg_mL_ESI.raw?rlkey=lpe648arsgoeipi95i578lvrd&dl=0
What I am trying to make a computer code do is change the time period into three specific time periods: 3-40 min, 40-65 min, and 65-100 min. Please let me know if you need me to provide more specific directions. I am happy to set up a video call to better explain the process I was hoping this computer code could execute.
Mohammad Imam Thank you for sharing this python library with me, I will give it a shot, but upon first glance, I am not trying to process m/z data, I am trying to process the light absorbance data.
Both of you, please let me know if you need more information/context from me. Thanks to you both for taking the time to try and address my request
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