Issue 337: mascot v2.4 MS1 import raw data

issues
Status:closed
Assigned To:Guest
Type:Defect
Area:Skyline
Priority:2
Milestone:2.6
Opened:2014-07-11 by alex
Changed:2014-08-28 by Brendan MacLean
Resolved:2014-08-28 by Brendan MacLean
Resolution:Not Repro
Closed:2014-08-28 by Brendan MacLean
2014-07-11 alex
Title»mascot v2.4 MS1 import raw data
Assigned To»Brendan MacLean
Type»Defect
Area»Skyline
Priority»2
Milestone»2.6
Hi Brendan,

I noticed a bug in MS1 filtering / spectra assignment when multiple spectra match to the same peptide. Here is my workflow:

1. search data using mascot 2.4
2. download .dat file
3. build reference genome in skyline
4. import spectral library
5. add all peptides to the document
6. import .raw file

In case there are more than one spectra, all other spectra are not assigned and an error message is displayed "Failure loading spectrum. Library might be corrupted."

.dat file contains a variable modification on D or E of C6N4H12O as well as variable M (oxidation) and static C (carbamidomethyl)
background proteome was digested with AspN, resulting in N-terminal peptides with D and E.

This error is reproducible on skyline-daily 64 bit 2.5.1.6484 (my PC) and skyline 2 64 bit (Watson).

Best, Alex.
 
 hebhardt_O1207_185.sky.zip
 hebhardt_O1207_185.dat
 ups1.fasta
 hebhardt_O1207_185.mgf

2014-07-11 Brendan MacLean
Assigned ToBrendan MacLean»kaipot@u.washington.edu
Kaipo, please have a look at this one.

2014-07-13 alex
ok, I have a theory regarding this bug: if the proteins in the background (set in skyline) don't match the proteins from the database searched (mascot), then this error occurs. My evidence: I matched now both databases and all spectra work fine (see attachment).

I hope this helps. At least now I have a solution to the posted problem.
Alex.
 
 hebhardt_O1207_185_v2.sky.zip

2014-08-28 Brendan MacLean
resolve as Not Repro
Statusopen»resolved
Assigned Tokaipot@u.washington.edu»ebhardt@imsb.biol.ethz.ch

2014-08-28 Brendan MacLean
close
Statusresolved»closed
Assigned Toebhardt@imsb.biol.ethz.ch»Guest