[spctools-discuss] Re: readw MS/MS precursor mass wrong

2009-09-09 Thread Dominik Schwudke
Dear Natalie, sorry for my last email. I had overseen that we have the wrong version again. Thank You again. Natalie Tasman wrote: Hello Dominik, Jimmy, Besides my recommendation to try msconvert, which is the program with more developer focus at this point, there is already a

[spctools-discuss] Re: readw MS/MS precursor mass wrong

2009-09-08 Thread Jimmy Eng
That 742.5391 precursor mass is the monoisotopic m/z mass recorded in the scan header of the raw file itself. readw just grabs this value, if present, via the thermo interface. No way to turn this off in readw (besides a relatively simple edit of the code and rebuilding the binary). Without

[spctools-discuss] Re: readw MS/MS precursor mass wrong

2009-09-08 Thread Matthew Chambers
Yeah, I'd like to see the isolation window from the triggering survey scan because it seems unlikely that the monoisotopic m/z would be less accurate than the filter's isolation m/z (except it might pick the a+1 peak, but that's almost certainly still better than the isolation m/z). -Matt

[spctools-discuss] Re: readw MS/MS precursor mass wrong

2009-09-08 Thread Dominik Schwudke
Dear Jimmy, the problem is that Thermo software is not especially intelligent by assigning the monoisotopic mass when a complex sample is analyzed. I actually would like to have the converter not making this decision. For that we have developed our own software. Can I somehow switch that

[spctools-discuss] Re: readw MS/MS precursor mass wrong

2009-09-08 Thread Natalie Tasman
Hello Dominik, Jimmy, Besides my recommendation to try msconvert, which is the program with more developer focus at this point, there is already a command-line option in the 4.3 series ReAdW program. I'd added this feature because Thermo's software did not understand which scan to report