ERROR: Error in SkylinetoMSstatsFormat

ERROR: Error in SkylinetoMSstatsFormat dayne0208  2021-05-07

I am attending 2021 May Institute proteomics workshop. I am following Ali skyline batch tutorial and received an error message at the end of log. What did I do wrong?

[5/7/2021 8:26:59 PM]    97% - Writing row 4,075,679/4,208,580
[5/7/2021 8:27:01 PM]    98% - Writing row 4,119,980/4,208,580
[5/7/2021 8:27:04 PM]    99% - Writing row 4,164,281/4,208,580
[5/7/2021 8:27:06 PM]    100%
[5/7/2021 8:27:06 PM]    Report MSstats Input-plus exported successfully to C:\NEU21_Skyline\Bruderer\Bruderer_ppm15c_rt10\MSstats Input-plus.csv.
[5/7/2021 8:27:07 PM]    Converting MSstats Input-plus to invariant format...
[5/7/2021 8:27:07 PM]    Reading MSstats Input-plus.csv
[5/7/2021 8:27:10 PM]    Updating MSstats Input-plus.csv
[5/7/2021 8:27:12 PM]    Saving MSstats Input-plus.csv
[5/7/2021 8:27:14 PM]    "C:\NEU21_Skyline\scripts\MSstats_Bruderer.R" "C:\NEU21_Skyline\Bruderer\Bruderer_ppm15c_rt10\MSstats Input-plus.csv"
[5/7/2021 8:27:18 PM]    
[5/7/2021 8:27:18 PM]    Reading  MSstats Input-plus.csv 
[5/7/2021 8:27:18 PM]    Attaching package: 'dplyr'
[5/7/2021 8:27:18 PM]    
[5/7/2021 8:27:18 PM]    The following objects are masked from 'package:stats':
[5/7/2021 8:27:18 PM]    
[5/7/2021 8:27:18 PM]        filter, lag
[5/7/2021 8:27:18 PM]    
[5/7/2021 8:27:18 PM]    The following objects are masked from 'package:base':
[5/7/2021 8:27:18 PM]    
[5/7/2021 8:27:18 PM]        intersect, setdiff, setequal, union
[5/7/2021 8:27:18 PM]    
[5/7/2021 8:27:55 PM]    Finished reading  
[5/7/2021 8:27:55 PM]     [1] ProteinName             PeptideSequence         PeptideModifiedSequence
[5/7/2021 8:27:55 PM]     [4] PrecursorCharge         PrecursorMz             FragmentIon            
[5/7/2021 8:27:55 PM]     [7] ProductCharge           ProductMz               IsotopeLabelType       
[5/7/2021 8:27:55 PM]    [10] Condition               BioReplicate            FileName               
[5/7/2021 8:27:55 PM]    [13] Area                    StandardType            Truncated              
[5/7/2021 8:27:55 PM]    [16] DetectionQValue        
[5/7/2021 8:27:55 PM]    <0 rows> (or 0-length row.names)
[5/7/2021 8:27:55 PM]    Converting to MSstats format 
[5/7/2021 8:28:07 PM]    ERROR: Error in SkylinetoMSstatsFormat(raw, filter_with_Qvalue = TRUE, qvalue_cutoff = 0.01,  : 
[5/7/2021 8:28:07 PM]      ** Please check annotation. Each MS run can't have multiple conditions or BioReplicates.
[5/7/2021 8:28:07 PM]    Execution halted
[5/7/2021 8:28:09 PM]    ------------------------------ Bruderer: Error -------------------------------
[5/7/2021 8:28:09 PM]    ------------------------------ Runtime: 01:06:47 -------------------------------

Nick Shulman responded:  2021-05-07
That error is saying that MSstats cannot figure out which BioReplicate and Condition a particular result file belongs to.
This could happen if you extracted chromatograms from the same file twice, and each of those times the result file was added to a different Replicate in Skyline.

If you would like, you could send us your Skyline document and we could figure out what is going wrong.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

If that .zip file is less than 50MB you can attach it to this support request.
Otherwise, you can upload it here:

-- Nick
dayne0208 responded:  2021-05-08
I likely extracted chromatograms from the same file twice since I ran the batch run twice. It failed the first time when my network was interrupted. How do I remove the previous extractions and make a fresh start?

Thank you
Nick Shulman responded:  2021-05-08
In Skyline, you can use the menu item:
Edit > Manage Results
to remove replicates from the document.
Brendan MacLean responded:  2021-05-08
For the batch processing, however, you can reset the processing by deleting or renaming the analysis folder. If you click the folder button in Skyline Batch, it will open a Windows File Explorer on the folder. From there you can navigate up to the parent folder and delete or rename the analysis with the problem.

I am not sure I fully understand how you ended up in this state, but I will try to reproduce it next week and see that the issue is fixed in Skyline Batch.

Thanks for reporting your experience.

dayne0208 responded:  2021-05-12
Thank you Brendan and Nick. Brendan's fix did work.