I can't find any mention in the documentation about if CiRT can be used for calibration. The workflow published last year briefly mentions them, but I'm not sure if I can use OpenSWATH to do that kind of analysis. In the list of required input files, I see "An assay library containing assays for all iRT peptides in TraML format.", which makes me guess that CiRT isn't feasible. It's unclear if this is required only for that particular example or for all SWATH analysis by OpenSWATH. I also searched the codebase for CiRT hoping for some variable names to contain that phrase and didn't get any results. Could a couple of sentences be added to the documentation making this explicit? Perhaps OpenSwathRTNormalizer needs to be used, but I'm confused if I can/should specify that to OpenSwathWorkflow.

pyprophet merge --out=merged.osw --subsample_ratio=1 *.osw does not work any more with 2.0.4, can you update the docu?

We are trying a new method using Thermo Exploris to acquire DIA-MS plasma runs with 21Da windows on a 5 minute gradient. When I tried to analyze this data using openswathworkflow against the Twin library, it seems to be having a hard time performing RT normalization and fails with a low rsq - see error below:

  Progress of 'Load TraML file':
  -- done [took 0.02 s (CPU), 0.03 s (Wall)] -- 
  Progress of 'Extract iRT chromatograms':
  -- done [took 0.14 s (CPU), 0.14 s (Wall)] -- 
  Progress of 'Retention time normalization':
Will analyse 10 peptides with a total of 56 transitions 
rsd < 0.0 
Intercept                                117.811
Slope                                    -0.504536
Squared pearson coefficient              0.292509
Value of the t-distribution              2.57058
Standard deviation of the residuals      13.8761
Standard error of the slope              0.139571
The X intercept                          233.503
The lower border of confidence interval  202.136
The higher border of confidence interval 376.309
Chi squared value                        6085.67
x mean                                   179.034
stand_error_slope/slope_                 -27.5026
Coefficient of Variation                 -15.3617
=========================================
rsq: 0.292509 points: 7
rsd < 0.0 
Intercept                                117.811
Slope                                    -0.504536
Squared pearson coefficient              0.292509
Value of the t-distribution              2.57058
Standard deviation of the residuals      13.8761
Standard error of the slope              0.139571
The X intercept                          233.503
The lower border of confidence interval  202.136
The higher border of confidence interval 376.309
Chi squared value                        6085.67
x mean                                   179.034
stand_error_slope/slope_                 -27.5026
Coefficient of Variation                 -15.3617
=========================================
rsd < 0.0 
Intercept                                81.7185
Slope                                    -0.349548
Squared pearson coefficient              0.246127
Value of the t-distribution              2.77645
Standard deviation of the residuals      10.6092
Standard error of the slope              0.111326
The X intercept                          233.783
The lower border of confidence interval  197.264
The higher border of confidence interval 631.554
Chi squared value                        3398.77
x mean                                   183.405
stand_error_slope/slope_                 -30.3511
Coefficient of Variation                 -16.5487
=========================================
rsq: 0.246127 points: 6
rsd < 0.0 
Intercept                                81.7185
Slope                                    -0.349548
Squared pearson coefficient              0.246127
Value of the t-distribution              2.77645
Standard deviation of the residuals      10.6092
Standard error of the slope              0.111326
The X intercept                          233.783
The lower border of confidence interval  197.264
The higher border of confidence interval 631.554
Chi squared value                        3398.77
x mean                                   183.405
stand_error_slope/slope_                 -30.3511
Coefficient of Variation                 -16.5487
=========================================
rsd < 0.0 
Intercept                                67.8974
Slope                                    -0.229684
Squared pearson coefficient              0.226375
Value of the t-distribution              3.18245
Standard deviation of the residuals      6.01437
Standard error of the slope              0.0652778
The X intercept                          295.612
The lower border of confidence interval  233.667
The higher border of confidence interval 1406.64
Chi squared value                        1530.43
x mean                                   178.96
stand_error_slope/slope_                 -26.1854
Coefficient of Variation                 -14.632
=========================================
rsq: 0.226375 points: 5
rsd < 0.0 
Intercept                                67.8974
Slope                                    -0.229684
Squared pearson coefficient              0.226375
Value of the t-distribution              3.18245
Standard deviation of the residuals      6.01437
Standard error of the slope              0.0652778
The X intercept                          295.612
The lower border of confidence interval  233.667
The higher border of confidence interval 1406.64
Chi squared value                        1530.43
x mean                                   178.96
stand_error_slope/slope_                 -26.1854
Coefficient of Variation                 -14.632
=========================================
Error: Unexpected internal error (WARNING: rsq: 0.226374750572749 is below limit of 0.94999999999999996. Validate assays for RT-peptides and adjust the limit for rsq or coverage.)

I was able to check that all the iRT peptides were detected using QuiC and Skyline.
.

Any advice on why the Rsq normalization would fail on very short gradients (5 minute) and if there are any parameters i can try to adjust to proceed further would be highly appreciated.

Hi

I tried to run OpenSwathWorkflow on a bunch of DIA files (in mzML format) using a pqp library and an iRT.tsv file.

I am using OSW from the OMS 2.5 release.

For 19/20 file OSW went through producing functional .osw files.

However for one of the input files i received the following error and OSW crashed.

Loaded 18738 proteins, 216044 compounds with 1296264 transitions.
Loading mzML file in/MST132_raw.mzML using readoptions cache
Will analyze the metadata first to determine the number of SWATH windows and the window sizes.
Determined there to be 52 SWATH windows and in total 2519 MS1 spectra
Determined there to be 52 SWATH windows and in total 2519 MS1 spectra
Will load iRT transitions and try to find iRT peptides
Warning: Found multiple peptide sequences for peptide label group light. This is most likely an error and to fix this, a new peptide label group will be inferred - to override this decision, please use the override_group_label_check parameter.
Will analyse 20 peptides with a total of 100 transitions

mz regression parameters: Y = -1.23697 + -0.00131831 X + 0 X^2

sum residual sq ppm before 124.966 / after 53.8444
Will analyze 1296264 transitions in total.
Thread 0_0 will analyze 1959 compounds and 11754 transitions from SWATH 1 (batch 0 out of 1)
Thread 0_0 will analyze 1959 compounds and 11754 transitions from SWATH 1 (batch 1 out of 1)
Thread 0_0 will analyze 2212 compounds and 13272 transitions from SWATH 2 (batch 0 out of 2)
Thread 0_0 will analyze 2212 compounds and 13272 transitions from SWATH 2 (batch 1 out of 2)
Thread 0_0 will analyze 2212 compounds and 13272 transitions from SWATH 2 (batch 2 out of 2)
Thread 0_0 will analyze 2508 compounds and 15048 transitions from SWATH 3 (batch 0 out of 2)
Thread 0_0 will analyze 2508 compounds and 15048 transitions from SWATH 3 (batch 1 out of 2)
Thread 0_0 will analyze 2508 compounds and 15048 transitions from SWATH 3 (batch 2 out of 2)
WARNING in SignalToNoiseEstimatorMedian: 100% of all windows were sparse. You should consider increasing 'win_len' or decreasing 'min_required_elements'
Thread 0_0 will analyze 2695 compounds and 16170 transitions from SWATH 4 (batch 0 out of 2)
Thread 0_0 will analyze 2695 compounds and 16170 transitions from SWATH 4 (batch 1 out of 2)
Thread 0_0 will analyze 2695 compounds and 16170 transitions from SWATH 4 (batch 2 out of 2)
Thread 0_0 will analyze 2972 compounds and 17832 transitions from SWATH 5 (batch 0 out of 2)
Thread 0_0 will analyze 2972 compounds and 17832 transitions from SWATH 5 (batch 1 out of 2)
Thread 0_0 will analyze 2972 compounds and 17832 transitions from SWATH 5 (batch 2 out of 2)
Thread 0_0 will analyze 3322 compounds and 19932 transitions from SWATH 6 (batch 0 out of 3)
Thread 0_0 will analyze 3322 compounds and 19932 transitions from SWATH 6 (batch 1 out of 3)
Thread 0_0 will analyze 3322 compounds and 19932 transitions from SWATH 6 (batch 2 out of 3)

FATAL: uncaught exception!

last entry in the exception handler:
exception of type IllegalArgument occured in line 112, function static void OpenMS::SqliteConnector::executeStatement(sqlite3*, const OpenMS::String&) of /opt/conda/conda-bld/openms-meta_1599077223540/work/src/openms/source/FORMAT/SqliteConnector.cpp
error message: no such column: inf

Any idea what could have happened here?

In the Tutorial section of the Percolator adapter documentation, there are a couple of commands shown for PyProphet. Is this an unintentional copy of the instructions from the PyProphet documentation?

When I run openswath2.4.0, I encountered an error : Unexpected internal error (There were not enough bins with the minimal number of peptides). Is there any parameter that can be adjusted?

I have generated osw output files from OpenSwath 2.3 according to http://www.openswath.org/en/latest/docs/openswath_workflow.html. When running pyprophet merge (from https://github.com/grosenberger/pyprophet.git@feature/refactoring) according to
http://www.openswath.org/en/latest/docs/pyprophet.html i get the following error message:

$ pyprophet merge --out=merged.osw TM*.osw
Traceback (most recent call last):
File "/usr/local/bin/pyprophet", line 9, in
load_entry_point('pyprophet==2.0.0', 'console_scripts', 'pyprophet')()
File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 722, in call
return self.main(*args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 1092, in invoke
rv.append(sub_ctx.command.invoke(sub_ctx))
File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/pyprophet/main.py", line 201, in merge
merge_osw(infiles, outfile, subsample_ratio, global_reduce, test)
File "/usr/local/lib/python2.7/dist-packages/pyprophet/levels_contexts.py", line 137, in merge_osw
c.execute('DELETE FROM RUN')
sqlite3.OperationalError: no such table: RUN

Thanks,
Christofer

The documentation webpage recommends "For technical help with the libraries, please contact the SWATHAtlas team." But, there's no hyperlink to a webpage containing the team's contact details. Also, the navigation bar on the left side of the SWATHAtlas website contains no Contact Us section, so neither the OpenSWATH documentation nor the SWATHAtlas website provide any contact details.

In the tutorial http://openswath.org/en/latest/docs/docker.html , I followed this
# Generate tutorial container (osw_tutorial) and log in
docker run --name osw_tutorial --rm -v ~/Desktop/:/data -i -t openswath/openswath:0.1.1

and got this

root@ac42d8ff4c:/# .

what should I input to log in?

Thanks.

Hi，

I used "pyprophet export " to export the legacy.tsv file .And I did't find any result in my path.

Maybe could you give me some instructions about the condition?
Thanks !
Clover