From 39f924ea34b9113ebc96ec5e8a37ecea458a62d9 Mon Sep 17 00:00:00 2001 From: Marie Locard-Paulet <8386272+mlocardpaulet@users.noreply.github.com> Date: Thu, 12 Dec 2024 10:58:21 +0100 Subject: [PATCH 1/4] add links for DDA ions --- docs/available-modules/2-quant-lfq-ion-dda.md | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/docs/available-modules/2-quant-lfq-ion-dda.md b/docs/available-modules/2-quant-lfq-ion-dda.md index 92bd6047..a0108729 100644 --- a/docs/available-modules/2-quant-lfq-ion-dda.md +++ b/docs/available-modules/2-quant-lfq-ion-dda.md @@ -18,7 +18,16 @@ Other modules will be more suited to explore further post-pocessing steps. A subset of the Q Exactive HF-X Orbitrap (Thermo Fisher) data dependent acquisition (DDA) data described by [Van Puyvelde et al., 2022](https://www.nature.com/articles/s41597-022-01216-6) was used as a benchmark dataset. Here, only the first biological replicate series (named “alpha”) was used, encompassing three technical replicates of two different conditions (referred to as “A” and “B”). The samples are a mixture of commercial peptide digest standards of the following species: Escherichia coli (P/N:186003196, Waters Corporation), Yeast (P/N: V7461, Promega) and Human (P/N: V6951, Promega), with logarithmic fold changes (log2FCs) of 0, −1 and 2 for respectively Human, Yeast and E.coli. Please refer to the original publication for the full description of sample preparation and data acquisition parameters ([Van Puyvelde et al., 2022](https://www.nature.com/articles/s41597-022-01216-6)). -The files can be downloaded from the proteomeXchange repository [PXD028735](https://www.ebi.ac.uk/pride/archive/projects/PXD028735) or you can download them from the ProteoBench server here: [proteobench.cubimed.rub.de/datasets/raw_files/DDA/](https://proteobench.cubimed.rub.de/datasets/raw_files/DDA/) +The files can be downloaded from the proteomeXchange repository [PXD028735](https://www.ebi.ac.uk/pride/archive/projects/PXD028735), make sure that you download the following raw files: + +- [LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.raw) +- [LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.raw) +- [LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.raw) +- [LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.raw) +- [LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.raw) +- [LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.raw](https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD028735/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.raw) + +Alternatively, you can download them from the ProteoBench server here: [proteobench.cubimed.rub.de/datasets/raw_files/DDA/](https://proteobench.cubimed.rub.de/datasets/raw_files/DDA/) **It is imperative not to rename the files once downloaded!** From 2a880783406d9b6d1291a46f00d2680e1be5a5a8 Mon Sep 17 00:00:00 2001 From: Marie Locard-Paulet <8386272+mlocardpaulet@users.noreply.github.com> Date: Thu, 12 Dec 2024 11:03:36 +0100 Subject: [PATCH 2/4] add info for DIA --- docs/available-modules/4-quant-lfq-ion-dia-aif.md | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/docs/available-modules/4-quant-lfq-ion-dia-aif.md b/docs/available-modules/4-quant-lfq-ion-dia-aif.md index afccc71e..d8548488 100644 --- a/docs/available-modules/4-quant-lfq-ion-dia-aif.md +++ b/docs/available-modules/4-quant-lfq-ion-dia-aif.md @@ -1,6 +1,6 @@ # DIA quantification - precursor ions - AIF data -This module compares the sensitivity and quantification accuracy for data-independent acquisition (DIA) data, namely All-Ion Fragmentation, on a Q Exactive HF-X Orbitrap (Thermo Fisher). +This module compares the sensitivity and quantification accuracy for data-independent acquisition (DIA) data, namely All-Ion Fragmentation (AIF), on a Q Exactive HF-X Orbitrap (Thermo Fisher). Users can load their data and inspect the results privately. They can also make their outputs public by providing the associated parameter file and submitting the benchmark run to ProteoBench. By doing so, their workflow output will be stored alongside all other benchmark runs in ProteoBench and will be accessible to the entire community. **This module is not designed to compare later-stages post-processing of quantitative data such as missing value replacement, and we advise users to publically upload data without replacement of missing values and without manual filtering.** @@ -8,7 +8,6 @@ Users can load their data and inspect the results privately. They can also make We think that this module is more suited to evaluate the impact of (non exhaustive list): - search engine identification - peak picking -- match between run - low-level ion signal normalisation Other modules will be more suited to explore further post-pocessing steps. @@ -18,7 +17,16 @@ Other modules will be more suited to explore further post-pocessing steps. A subset of the Q Exactive HF-X Orbitrap (Thermo Fisher) data independent acquisition (DIA) data described by [Van Puyvelde et al., 2022](https://www.nature.com/articles/s41597-022-01216-6) was used as a benchmark dataset (in the manuscript referred to as All-Ion Fragmentation (AIF)). Here, only the first biological replicate series (named “alpha”) was used, encompassing three technical replicates of two different conditions (referred to as “A” and “B”). The samples are a mixture of commercial peptide digest standards of the following species: Escherichia coli (P/N:186003196, Waters Corporation), Yeast (P/N: V7461, Promega) and Human (P/N: V6951, Promega), with logarithmic fold changes (log2FCs) of 0, −1 and 2 for respectively Human, Yeast and E.coli. Please refer to the original publication for the full description of sample preparation and data acquisition parameters ([Van Puyvelde et al., 2022](https://www.nature.com/articles/s41597-022-01216-6)). -The files can be downloaded from the proteomeXchange repository PXD028735 (https://www.ebi.ac.uk/pride/archive/projects/PXD028735) or you can download them from the ProteoBench server here: https://proteobench.cubimed.rub.de/datasets/raw_files/DIA/ +The files can be downloaded from the proteomeXchange repository [PXD028735](https://www.ebi.ac.uk/pride/archive/projects/PXD028735), make sure that you download the following raw files: + +- [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) + +Alternatively, you can download them from the ProteoBench server here: [proteobench.cubimed.rub.de/datasets/raw_files/DDA/](https://proteobench.cubimed.rub.de/datasets/raw_files/DIA/) **It is imperative not to rename the files once downloaded!** From 0aad9c73770549377c2c31b800621ae5dd7f9093 Mon Sep 17 00:00:00 2001 From: Marie Locard-Paulet <8386272+mlocardpaulet@users.noreply.github.com> Date: Thu, 12 Dec 2024 11:09:12 +0100 Subject: [PATCH 3/4] homogenise module input tabs --- .../Quant/lfq/ion/DDA/input_file_description.md | 6 +++++- .../Quant/lfq/ion/DIA/AIF/input_file_description.md | 8 ++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/webinterface/pages/markdown_files/Quant/lfq/ion/DDA/input_file_description.md b/webinterface/pages/markdown_files/Quant/lfq/ion/DDA/input_file_description.md index 8693b8f1..3b551d2e 100644 --- a/webinterface/pages/markdown_files/Quant/lfq/ion/DDA/input_file_description.md +++ b/webinterface/pages/markdown_files/Quant/lfq/ion/DDA/input_file_description.md @@ -1,3 +1,7 @@ Please upload the output of your analysis, and indicate what software -tool it comes from (this is necessary to correctly parse your table - find more information in the "[How to use](https://proteobench.readthedocs.io/en/latest/available-modules/2-quant-lfq-ion-dda/#how-to-use)" section of this module. For the data to run your workflow on please see the section "[Data set](https://proteobench.readthedocs.io/en/latest/available-modules/2-quant-lfq-ion-dda/#data-set)". You can download an (*incomplete*) MaxQuant file example [here](https://raw.githubusercontent.com/Proteobench/ProteoBench/refs/heads/main/test/data/dda_quant/MaxQuant_2_5_1_evidence_sample.txt). \ No newline at end of file +tool it comes from (this is necessary to correctly parse your table) - find more information in the "[How to use](https://proteobench.readthedocs.io/en/latest/available-modules/2-quant-lfq-ion-dda/#how-to-use)" section of this module. To the raw data to run your workflow on please see the section "[Data set](https://proteobench.readthedocs.io/en/latest/available-modules/2-quant-lfq-ion-dda/#data-set)". You can download an (*incomplete*) MaxQuant file example [here](https://raw.githubusercontent.com/Proteobench/ProteoBench/refs/heads/main/test/data/dda_quant/MaxQuant_2_5_1_evidence_sample.txt) for testing. + +Remember: contaminant sequences are already present in the fasta file +associated to this module. **Do not add other contaminants** to your +search. This is important when using MaxQuant and FragPipe, among other tools. \ No newline at end of file diff --git a/webinterface/pages/markdown_files/Quant/lfq/ion/DIA/AIF/input_file_description.md b/webinterface/pages/markdown_files/Quant/lfq/ion/DIA/AIF/input_file_description.md index 7909806e..5d5c450c 100644 --- a/webinterface/pages/markdown_files/Quant/lfq/ion/DIA/AIF/input_file_description.md +++ b/webinterface/pages/markdown_files/Quant/lfq/ion/DIA/AIF/input_file_description.md @@ -1,9 +1,5 @@ -Please upload the ouput of your analysis, and indicate what software -tool it comes from (this is necessary to correctly parse your table - find -more information in the "[How to use](https://proteobench.readthedocs.io/en/stable/available-modules/4-quant-lfq-ion-dia-aif/)" -section of this module). - -Currently, we support output files from AlphaDIA, DIA-NN, FragPipe, MSAID, MaxQuant and Spectronaut. It is also possible to reformat your data in a tab-delimited file that we call "custom format" in the [documentation](https://proteobench.readthedocs.io/en/latest/available-modules/4-quant-lfq-ion-dia-aif/). +Please upload the output of your analysis, and indicate what software +tool it comes from (this is necessary to correctly parse your table) - find more information in the "[How to use](https://proteobench.readthedocs.io/en/latest/available-modules/4-quant-lfq-ion-dia-aif/#how-to-use)" section of this module. To the raw data to run your workflow on please see the section "[Data set](https://proteobench.readthedocs.io/en/latest/available-modules/4-quant-lfq-ion-dia-aif/#data-set)". Remember: contaminant sequences are already present in the fasta file associated to this module. **Do not add other contaminants** to your From ba7f6ecfd6b30d5ed63b80cbd89310938eb6190e Mon Sep 17 00:00:00 2001 From: Marie Locard-Paulet <8386272+mlocardpaulet@users.noreply.github.com> Date: Thu, 12 Dec 2024 11:14:08 +0100 Subject: [PATCH 4/4] amend markdown for peptidoform module --- .../Quant/lfq/peptidoform/DDA/input_file_description.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/webinterface/pages/markdown_files/Quant/lfq/peptidoform/DDA/input_file_description.md b/webinterface/pages/markdown_files/Quant/lfq/peptidoform/DDA/input_file_description.md index b5eaa50a..43270ba2 100644 --- a/webinterface/pages/markdown_files/Quant/lfq/peptidoform/DDA/input_file_description.md +++ b/webinterface/pages/markdown_files/Quant/lfq/peptidoform/DDA/input_file_description.md @@ -1,3 +1,6 @@ - Please upload the output of your analysis, and indicate what software -tool it comes from (this is necessary to correctly parse your table - find more information in the "[How to use](https://proteobench.readthedocs.io/en/latest/available-modules/3-quant-lfq-peptidoform-dda/#how-to-use)" section of this module. For the data to run your workflow on please see the section "[Data set](https://proteobench.readthedocs.io/en/latest/available-modules/3-quant-lfq-peptidoform-dda/#data-set)". \ No newline at end of file +tool it comes from (this is necessary to correctly parse your table) - find more information in the "[How to use](https://proteobench.readthedocs.io/en/latest/available-modules/3-quant-lfq-peptidoform-dda)" section of this module. To the raw data to run your workflow on please see the section "[Data set](https://proteobench.readthedocs.io/en/latest/available-modules/3-quant-lfq-peptidoform-dda)". + +Remember: contaminant sequences are already present in the fasta file +associated to this module. **Do not add other contaminants** to your +search. This is important when using MaxQuant and FragPipe, among other tools. \ No newline at end of file