From 287eb507817ee6d88d6d2a2f830f61d021bd8e40 Mon Sep 17 00:00:00 2001 From: Marie Locard-Paulet <8386272+mlocardpaulet@users.noreply.github.com> Date: Sat, 16 Sep 2023 13:44:06 +0200 Subject: [PATCH 1/2] Update DDA_Quant.py add information regarding DDA quan module in streamlit interface --- webinterface/pages/DDA_Quant.py | 39 ++++++++++++++++++++++++++++++++- 1 file changed, 38 insertions(+), 1 deletion(-) diff --git a/webinterface/pages/DDA_Quant.py b/webinterface/pages/DDA_Quant.py index 91398185..ea28ff60 100644 --- a/webinterface/pages/DDA_Quant.py +++ b/webinterface/pages/DDA_Quant.py @@ -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"): From 9d7397e92ab87b6e2107cf638de91bc2d53e54c4 Mon Sep 17 00:00:00 2001 From: Marie Locard-Paulet <8386272+mlocardpaulet@users.noreply.github.com> Date: Sun, 17 Sep 2023 16:17:39 +0200 Subject: [PATCH 2/2] use triple quotes for textblock instead of escaping new line --- webinterface/pages/DDA_Quant.py | 76 ++++++++++++++++++--------------- 1 file changed, 42 insertions(+), 34 deletions(-) diff --git a/webinterface/pages/DDA_Quant.py b/webinterface/pages/DDA_Quant.py index ea28ff60..22d3ff7c 100644 --- a/webinterface/pages/DDA_Quant.py +++ b/webinterface/pages/DDA_Quant.py @@ -76,41 +76,49 @@ def _main_page(self): """Format main page.""" 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.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). + 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: + - To estimate the sensitivity of the workflows, we report the + number of unique precursors (charged modified sequence) quantified + in all 6 runs. + - To estimate the accuracy of the workflows, we report the weighted + sum of precursor deviation from expected ratios. + - To estimate the precision of the workflows, we report the weighted + average of the interquartile range (IQR) of the precursors ratio. + + 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. + 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.markdown(""" + The raw files used for this module were acquired on an Orbitrap + Q-Exactive H-FX (ThermoScientific). They can be downloaded from the + proteomeXchange repository PXD028735. You can download them here: + [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) + [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) + [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) + [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) + [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) + [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) + + **It is imperative not to rename the files once downloaded!** + """) + st.markdown(""" + Download the fasta file here: [TODO] + 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")