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I'm using FragPipe 18.0 to process some DDA data to generate spectral library, and found some peptides that are not in the digestion rule of stricttrypsin appeared in final library. In further exploration, these peptides might more likely from decoy sequences but not forward ones
Here are some examples
Library peptide IHTGSLR is from protein Q9R1X5, and the sequence with +-5 AAs per side is EEGKQIHTGSLRLQRTL. The AA before this peptide is Q but not KR
The reversed peptide of it is LSGTHIK and is only included in protein Q7TPM9, and the +-5 AAs seq is IILPRLSGTHIKLWKLC. In this case, the previous AA is R
In related pepxml from msfragger, IHTGSLR primarily belongs to rev_sp|Q7TPM9|MTMRA_MOUSE and alternatively belongs to sp|Q9R1X5|MRP5_MOUSE
Peptide LDLALSR is from Q810B6, and the +-5 seq is NGDLALDLALSRRLESI
With K/R conversion, the reversed peptide SLALDLK is in O09174 and Q5DTH5, and the +-5 seqs are ARGKRSLALDLKRSQGV and ESCWSSLALDLKKSNSA (the former one matched digestion rule)
In related pepxml from msfragger, LDLALSR primarily belongs to rev_sp|O09174|AMACR_MOUSE and alternatively belongs to sp|Q810B6|ANFY1_MOUSE
There are 26 peptides like above ones found in the final library which has total 179672 peptides. This case happened in FP 18.0 (with msfragger 3.5, philosopher 4.4.0, easypqp 0.1.30), but not in FP 17.1 (with msfragger 3.4, philosopher 4.1.0, easypqp 0.1.26, and this was ran half year ago). DIA_SpecLib_Quant was loaded in both two versions of FP
The only difference I could observe in pepxml files from two versions is these peptides would have alternative proteins (and they are forward ones) written along with search hits in 18.0 while only decoy proteins as primary in 17.1
I'm wondering if this is caused by my unintentionally changed settings or the processing approaches in the workflow are changed
Best,
Ronghui
Upload your log file
(If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)
Dear FragPipe team,
I'm using FragPipe 18.0 to process some DDA data to generate spectral library, and found some peptides that are not in the digestion rule of stricttrypsin appeared in final library. In further exploration, these peptides might more likely from decoy sequences but not forward ones
Here are some examples
IHTGSLR
is from proteinQ9R1X5
, and the sequence with +-5 AAs per side isEEGKQIHTGSLRLQRTL
. The AA before this peptide is Q but not KRLSGTHIK
and is only included in proteinQ7TPM9
, and the +-5 AAs seq isIILPRLSGTHIKLWKLC
. In this case, the previous AA is RIHTGSLR
primarily belongs torev_sp|Q7TPM9|MTMRA_MOUSE
and alternatively belongs tosp|Q9R1X5|MRP5_MOUSE
LDLALSR
is fromQ810B6
, and the +-5 seq isNGDLALDLALSRRLESI
SLALDLK
is inO09174
andQ5DTH5
, and the +-5 seqs areARGKRSLALDLKRSQGV
andESCWSSLALDLKKSNSA
(the former one matched digestion rule)LDLALSR
primarily belongs torev_sp|O09174|AMACR_MOUSE
and alternatively belongs tosp|Q810B6|ANFY1_MOUSE
There are 26 peptides like above ones found in the final library which has total 179672 peptides. This case happened in FP 18.0 (with msfragger 3.5, philosopher 4.4.0, easypqp 0.1.30), but not in FP 17.1 (with msfragger 3.4, philosopher 4.1.0, easypqp 0.1.26, and this was ran half year ago). DIA_SpecLib_Quant was loaded in both two versions of FP
The only difference I could observe in pepxml files from two versions is these peptides would have alternative proteins (and they are forward ones) written along with search hits in 18.0 while only decoy proteins as primary in 17.1
I'm wondering if this is caused by my unintentionally changed settings or the processing approaches in the workflow are changed
Best,
Ronghui
(If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)
Here are two log files, and I'd like to share other files via email if you want
log-FP17.1.txt
log-FP18.0.txt
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