You can type some examples SDRF and let us know and we can let you know what it does and hep to fixed it

OK.

Thanks Yasset, sorry for the delay, I was able to make one sample sheet that seems to work but I would like advises on whether it make sense as well as what woudl be the minimal set of column that would work... Here's what seems to work for a 10 plex TMT of cancer samples

test.sdrf.tsv

Looks ok. Hi #C02Q3FL29PD we are discussing in the SDRF format forum how the format should look in the next iteration and 1.1.0, and Julianus took this idea https://github.com/bigbio/proteomics-sample-metadata/issues/788 if you are a user of quantms and would like to give our opinion from the pipeline point of view on how this can help to prepare better the format for quantms, let us know. Also, feel free to create issues about the format in relation to quantms, its creation, etc.

Hi there 🙂

According to the quantms 1.7.0 documentation, the parameter

-c verbose_modules

is required to output detailed intermediate files.

However, I suspect there might be an error here. Shouldn't the correct command be

-profile verbose_modules

?

My reasoning is as follows:

-c

is a basic Nextflow parameter that requires a configuration file to be specified afterward. After reviewing the quantms source code, I found that a

profile verbose_modules

is defined within the

nextflow.config

file. Therefore, the correct invocation should be

-profile verbose_modules

.

You are totally rigth @lilin, I will change this in the doc.

Hi there~ I encountered an error when running multiQC while using quantms 1.7.0.

nextflow run -offline -bg -profile docker,verbose_modules -params-file ./params.json /data_5t/lilin/pipelines-preuse/quantms/quantms-1.7.0/main.nf

╭──────────────── Oops! The 'pmultiqc' MultiQC module broke... ────────────────╮ │ Please copy this log and report it at │ │ https://github.com/MultiQC/MultiQC/issues │ │ Please attach a file that triggers the error. The last file found was: │ │ results/PXD001819_v1.sdrf_openms_design_msstats_in.csv │ │ │ │ Traceback (most recent call last): │ │ File "/usr/local/lib/python3.12/site-packages/multiqc/core/exec_modules.py │ │ these_modules: Union[BaseMultiqcModule, List[BaseMultiqcModule]] = modul │ │ ^^^^^ │ │ File "/usr/local/lib/python3.12/site-packages/pmultiqc/modules/core/core.p │ │ quantms.draw_plots() │ │ File "/usr/local/lib/python3.12/site-packages/pmultiqc/modules/quantms/qua │ │ draw_oversampling( │ │ File "/usr/local/lib/python3.12/site-packages/pmultiqc/modules/common/plot │ │ bar_html = bargraph.plot(data=oversampling, cats=oversampling_plot, pcon │ │ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ │ │ File "/usr/local/lib/python3.12/site-packages/multiqc/plots/bargraph.py", │ │ plot = BarPlot.from_inputs(inputs) │ │ ^^^^^^^^^^^^^^^^^^^^^^^^^^^ │ │ File "/usr/local/lib/python3.12/site-packages/multiqc/plots/bargraph.py", │ │ return BarPlot.create( │ │ ^^^^^^^^^^^^^^^ │ │ File "/usr/local/lib/python3.12/site-packages/multiqc/plots/bargraph.py", │ │ model: Plot[Dataset, BarPlotConfig] = Plot.initialize( │ │ ^^^^^^^^^^^^^^^^ │ │ File "/usr/local/lib/python3.12/site-packages/multiqc/plots/plot.py", line │ │ raise ValueError("No datasets to plot") │ │ ValueError: No datasets to plot │ │ │ ╰──────────────────────────────────────────────────────────────────────────────╯

do you have data input in the pmultiqc step?>

I think there should be data input — the file PXD001819_v1.sdrf_openms_design_msstats_in.csv mentioned above has content in it.

I think the SDRF is wrong? Can you provided us with a zip of the project in here: https://github.com/bigbio/pmultiqc/issues for us to debug pmultiqc. For now you can skip pmultiqc step if you want/

sure. Here is the SDRF file I used

Hi #C02Q3FL29PD users we have two announcements ongoing: 1- https://github.com/bigbio/quantms/issues/700 We will remove Msstats from the workflow; differential expression will need to happen in an external component/workflow 2- https://github.com/bigbio/quantms/issues/697 DIA workflow part will be remove in favor of quantmsdiann https://github.com/bigbio/quantmsdiann

Release of quantmsdiann 2.0.0 https://github.com/bigbio/quantmsdiann/releases/tag/v2.0.0

Hi #C02Q3FL29PD Has anyone used a CSV to run quantms 1.7? If yes, can you please share your experience? How is the fraction identifier taken into account since it is not given by the CSV. Thank you !

what do you mean the csv? SDRF?

https://docs.quantms.org/input/ Here in the documentation, there is a samplesheet CSV to be submitted instead of the SDRF

Go it; I think I have to update the docs; we have an internal discussions to remove the csv; and also @Julianus Pfeuffer is working in a more sdrflite format that can help with this. What are your requirements? why you can't use SDRF?

Okay, thank you! I just thought it would be easier to use a CSV instead of an SDRF

Hello #C02Q3FL29PD Does anyone here still use PrideInspector Toolsuite for MS/MS validation ? Can you please share your experience or with any other open source tool Thank you in advance!

No; it has been deprecated long time ago.

We are planning to produce a simple tool to inspect quantms results.

Hello #C02Q3FL29PD Has anyone hit this error when running

ProteomicsLFQ

with _`targeted_only false`_ ?

Error: Unexpected internal error (MinMZ,MaxMZ,MinRT,MaxRT values outside of sensible value ranges. Are they uninitialized? (1.712059244374231e-10/7.413142472324203e34/0.1477341/5400.264180000000124)

<WARNING in SignalToNoiseEstimatorMedian: 100% of all Signal-to-Noise estimates are too high, because the median was found in the rightmost histogram-bin. You should consider increasing 'max_intensity' (and maybe 'bin_count' with it, to keep bin width reasonable)> occurred 18 times

<Warning: Cannot integrate if spectrum is empty> occurred 4224696 times

can you please share your experience? Thank you !

Can you run it with more logger for us to check the feature with the issue @Timo Sachsenberg Can you check what could be happening here?

Hello @Yasset Perez Riverol Following my last question, when you run

ProteomicsLFQ

with _`targeted_only false`,_ does it do the MBR based on the factor value column (or any other column grouping samples alike) or based on all samples in the sdrf? because it seems to me that it does the MBR on all samples, which might cause the error I submitted (in this case, it will fully make sense).

Hello #C02Q3FL29PD, I am seeing the same issue on my side. In the case of fractionated datasets, should the fractions be separated manually and processed independently to avoid a global MBR across all runs?

Hi, I was able to successfully run the quantms pipeline and got the qpx outputs. I was attempting to use these with mokume but ran across several issues. Every feature in the feature.parquet file has

unique = null

. Current mokume requires

unique = true

, leaving zero features and causing a later DirectLFQ division-by-zero error. There is also the issue of peptide counts needed for deqms processing, which I'm not sure if this processing step computes that.

Are really all the features annoted ad unique = null and also features I think in mokume are read without the need of that column; can you report the issue in mokume probably report the file to the developers.

Hello @Yasset Perez Riverol I have a question, please. Is it normal to have NA in _protein_coverage_ column of the mzTAB for TMT data (using quantms 1.7.0)?

yes because we do't process the protein coverage; in the new dev version we are computing that information.