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Error with MSstats_Bruderer.R script

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Error with MSstats_Bruderer.R script dayne0208  2021-05-12 03:56
 

Hi,
I am attending 2021 May Institute proteomics workshop. I am following Ali skyline batch tutorial and received an error message during the MSstats_Bruderer.R script phase. What did I do wrong? I've also attached a full copy of the log and MSstats Input-plus.csv files.

[5/11/2021 10:21:57 PM] Saving MSstats Input-plus.csv
[5/11/2021 10:22:22 PM] "C:\Users\dayne\Documents\May2021\MacLean_L3\NEU21_Skyline\scripts\MSstats_Bruderer.R" "C:\Users\dayne\Documents\May2021\MacLean_L3\NEU21_Skyline\Bruderer\Bruderer_ppm15c_rt10\MSstats Input-plus.csv"
[5/11/2021 10:22:28 PM] Reading MSstats Input-plus.csv
[5/11/2021 10:22:28 PM]
[5/11/2021 10:22:28 PM] Attaching package: 'dplyr'
[5/11/2021 10:22:28 PM]
[5/11/2021 10:22:28 PM] The following objects are masked from 'package:stats':
[5/11/2021 10:22:28 PM]
[5/11/2021 10:22:28 PM] filter, lag
[5/11/2021 10:22:28 PM]
[5/11/2021 10:22:28 PM] The following objects are masked from 'package:base':
[5/11/2021 10:22:28 PM]
[5/11/2021 10:22:28 PM] intersect, setdiff, setequal, union
[5/11/2021 10:22:28 PM]
[5/11/2021 10:23:02 PM] Finished reading
[5/11/2021 10:23:03 PM] [1] ProteinName PeptideSequence PeptideModifiedSequence
[5/11/2021 10:23:03 PM] [4] PrecursorCharge PrecursorMz FragmentIon
[5/11/2021 10:23:03 PM] [7] ProductCharge ProductMz IsotopeLabelType
[5/11/2021 10:23:03 PM] [10] Condition BioReplicate FileName
[5/11/2021 10:23:03 PM] [13] Area StandardType Truncated
[5/11/2021 10:23:03 PM] [16] DetectionQValue
[5/11/2021 10:23:03 PM] <0 rows> (or 0-length row.names)
[5/11/2021 10:23:03 PM] Converting to MSstats format
[5/11/2021 10:23:14 PM] ERROR: Error in SkylinetoMSstatsFormat(raw, filter_with_Qvalue = TRUE, qvalue_cutoff = 0.01, :
[5/11/2021 10:23:14 PM] ** Please check annotation. Each MS run can't have multiple conditions or BioReplicates.
[5/11/2021 10:23:14 PM] Execution halted
[5/11/2021 10:23:15 PM] ------------------------------ Bruderer: Error -------------------------------
[5/11/2021 10:23:15 PM] ------------------------------ Runtime: 16:31:03 -------------------------------
 
 
Nick Shulman responded:  2021-05-12 10:45
Another user ran into the same error here:
https://skyline.ms/announcements/home/support/thread.view?rowId=51055

This error can happen if the same result file has been added to the Skyline document more than once and therefore belongs to more than one Replicate.
Brendan gave some instructions in that other support request for how to deal with this.
-- Nick