Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update DDA_Quant.py #74

Merged
merged 2 commits into from
Sep 18, 2023
Merged

Update DDA_Quant.py #74

Changes from 1 commit
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
287eb50
Update DDA_Quant.py
mlocardpaulet Sep 16, 2023
9d7397e
use triple quotes for textblock instead of escaping new line
mlocardpaulet Sep 17, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
39 changes: 38 additions & 1 deletion webinterface/pages/DDA_Quant.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -74,7 +74,44 @@ def generate_input_field(self, input_format: str, content: dict):

def _main_page(self):
"""Format main page."""
st.title("Proteobench")
st.title("Module 2: DDA quantification")
st.header("Description of the module")
st.markdown("This module compares the MS1-level quantification tools for \
data-dependent acquisition (DDA). The raw files provided for \
this module are presented in the comprehensive LFQ benchmark \
dataset from [Van Puyvelde et al., 2022](https://www.nature.com/articles/s41597-022-01216-6). \n\
The samples contain tryptic peptides from Homo sapiens, \
Saccharomyces cerevisiae, and Escherichia coli, mixed in different \
ratios (condition A and condition B), with three replicates of each \
condition. With these samples, we calculate three metrics: \n\
* To estimate the sensitivity of the workflows, we report the \
number of unique precursors (charged modified sequence) quantified \
in all 6 runs. \n\
* To estimate the accuracy of the workflows, we report the weighted \
sum of precursor deviation from expected ratios. \n\
* To estimate the precision of the workflows, we report the weighted\
average of the interquartile range (IQR) of the precursors ratio.\n\
ProteoBench plots these three metrics to visualize workflow outputs\
from different tools, with different versions, and/or different \
sets of parameters for the search and quantification. \n\
The full description of the pre-processing steps and metrics \
calculation is available here: LINK.")
st.header("Downloading associated files")
st.markdown("The raw files used for this module were acquired on an Orbitrap \
Q-Ex H-FX (ThermoScientific). They can be downloaded from the \
proteomeXchange repository PXD028735. You can download them here: \n\
[LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01.raw) \n\
[LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02.raw) \n\
[LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03.raw) \n\
[LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01.raw) \n\
[LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02.raw) \n\
[LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03.raw) \n\
**It is imperative not to rename the files once downloaded!**")
st.markdown("Download the fasta file here: [TODO] \n\
The fasta file provided for this module contains the three species \
present in the samples and contaminant proteins \
([Frankenfield et al., JPR](https://pubs.acs.org/doi/10.1021/acs.jproteome.2c00145))")

st.header("Input and configuration")

with st.form(key="main_form"):
Expand Down
Loading