Menu
▾
▴
[Open-ms-general] Peak picking issues
|
From: Peter H. <ph...@cm...> - 2012-05-25 06:20:11
|
Hello, first off, I'm new to OpenMS and I'm finding it difficult to find my way through the program. I have gone through the tutorials and other documentation, but I'm still don't know what I'm doing wrong. I am generally very good with computers, but OpenMS is definitely causing me problems. Here's what I want to do. I have a Thermo RAW file that I'm converting to mzML with PWiz. I want to use OpenMS to use it's wonderful "PeakPickerWavelet" and then convert the result file to an MGF that I can use for input into several search algorithms. I eventually want to do this as a batch process so I can get lots of files processed sequentially. I thought I had worked out how to do the first part (peak picking) and used a simple TOPPAS workflow consisting of; Input file -> PeakPickerWavelet -> output file The log gave the output below and the file I ended up with did not have any peak information for the MS/MS scans. The MS scans were also missing a whole stack of the m/z and the masses were shifted. ie. when I compare the processed and original mzML files the processed scans do not reflect the original scan. When I run the PeakPickerWavelet in TOPPView it all works fine. I used the same parameters when I setup the workflow. I'm clearly doing something wrong, but I do not know what that may be. I'm using the 64-bit version under Win XP. Any and all assistance is gratefully received. Peter ============================================================================== 15:19:45 NOTICE: PeakPickerWavelet started. Processing ... ============================================================================== 15:19:45 NOTICE: PeakPickerWavelet finished! ============================================================================== 15:19:45 NOTICE: Entire pipeline execution finished! ============================================================================== 15:19:45 NOTICE: PeakPickerWavelet started. Processing ... While loading 'K:\Data\OrbiTrapVelos1\PGH\240412\MCS_2_2E_1_01.mzML': Unhandled cvParam 'MS:1000927' in tag 'scan'. While loading 'K:\Data\OrbiTrapVelos1\PGH\240412\MCS_2_2E_1_01.mzML': Unhandled attribute 'instrumentConfigurationRef' in 'scan' tag. width0 = 0.009375 width1 = 0.009375 width2 = 0.009375 average estimated width 0.009375 <While loading 'K:\Data\OrbiTrapVelos1\PGH\240412\MCS_2_2E_1_01.mzML': Unhandled attribute 'instrumentConfigurationRef' in 'scan' tag.> occurred 666 times <While loading 'K:\Data\OrbiTrapVelos1\PGH\240412\MCS_2_2E_1_01.mzML': Unhandled cvParam 'MS:1000927' in tag 'scan'.> occurred 5014 times While loading 'K:\Data\OrbiTrapVelos1\PGH\240412\MCS_2_2E_2_01.mzML': Unhandled cvParam 'MS:1000927' in tag 'scan'. While loading 'K:\Data\OrbiTrapVelos1\PGH\240412\MCS_2_2E_2_01.mzML': Unhandled attribute 'instrumentConfigurationRef' in 'scan' tag. width0 = 0.013125 width1 = 0.009375 width2 = 0.024375 average estimated width 0.015625 <While loading 'K:\Data\OrbiTrapVelos1\PGH\240412\MCS_2_2E_2_01.mzML': Unhandled attribute 'instrumentConfigurationRef' in 'scan' tag.> occurred 334 times <While loading 'K:\Data\OrbiTrapVelos1\PGH\240412\MCS_2_2E_2_01.mzML': Unhandled cvParam 'MS:1000927' in tag 'scan'.> occurred 4746 times While loading 'K:\Data\OrbiTrapVelos1\PGH\240412\MCS_2_2E_3_01.mzML': Unhandled cvParam 'MS:1000927' in tag 'scan'. While loading 'K:\Data\OrbiTrapVelos1\PGH\240412\MCS_2_2E_3_01.mzML': Unhandled attribute 'instrumentConfigurationRef' in 'scan' tag. width0 = 0.024375 width1 = 0.0225 width2 = 0.015 average estimated width 0.020625 <While loading 'K:\Data\OrbiTrapVelos1\PGH\240412\MCS_2_2E_3_01.mzML': Unhandled attribute 'instrumentConfigurationRef' in 'scan' tag.> occurred 233 times <While loading 'K:\Data\OrbiTrapVelos1\PGH\240412\MCS_2_2E_3_01.mzML': Unhandled cvParam 'MS:1000927' in tag 'scan'.> occurred 4663 times ============================================================================== 15:48:39 NOTICE: PeakPickerWavelet finished! ============================================================================== 15:48:39 NOTICE: Output file 'C:\Documents and Settings\phains\TOPPAS_out\003\MCS_2_2E_1_01.mzML' written. ============================================================================== 15:48:39 NOTICE: Output file 'C:\Documents and Settings\phains\TOPPAS_out\003\MCS_2_2E_2_01.mzML' written. ============================================================================== 15:48:39 NOTICE: Output file 'C:\Documents and Settings\phains\TOPPAS_out\003\MCS_2_2E_3_01.mzML' written. ============================================================================== 15:48:39 NOTICE: Entire pipeline execution finished! |