Hi,
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 -------------------------------