Issue 437: Improve performance of BlibBuild spectral library building from pepXML/mzXML

issues
Status:closed
Assigned To:Guest
Type:Todo
Area:BiblioSpec
Priority:2
Milestone:3.2
Opened:2015-11-08 by Brendan MacLean
Changed:2016-07-07 by Brendan MacLean
Resolved:2016-07-07 by Kaipo
Resolution:Fixed
Closed:2016-07-07 by Brendan MacLean
2015-11-08 Brendan MacLean
Title»Improve performance of BlibBuild spectral library building from pepXML/mzXML
Assigned To»kaipot@u.washington.edu
Type»Todo
Area»BiblioSpec
Priority»2
Milestone»3.2
It is currently taking way longer than it should to build spectral libraries from pepXML/mzXML for DIA-Umpire results searched with the TPP (an important use case). This appears to be due to the way we retrieve spectra from the mzXML file. We are currently enumerating the matched spectra and using random-access spectrum reading to retrieve the spectra from the mzXML file. It should be much faster to read all spectra in the file sequentially, skipping the ones for which we have no match and loading the ones for which we have a match. Sequential reading is always much faster in spinning media and can often be faster even on SSD, because random access rarely allows buffered reading, but instead must seek and load each spectrum individually.

2016-07-07 Kaipo
resolve as Fixed
Statusopen»resolved
Assigned Tokaipot@u.washington.edu»Brendan MacLean

2016-07-07 Brendan MacLean
close
Statusresolved»closed
Assigned ToBrendan MacLean»Guest