Hi Joachim [sorry for mistaking your name in my last e-mail], The data you sent does not show any problem with retention time. Only the formatting is different. Xcalibur shows retention time in minutes, while MZmine shows it according to the formatting settings in preferences. Your formatting pattern is set to "mm.ss" where mm means minutes and ss means seconds. Default pattern is MZmine is mm:ss (not mm.ss).
For example for scan #8 Xcalibur shows 5.088 minutes, while MZmine shows 5.05 (meaning 5 minutes and 5 seconds). 5.08 minutes = 5 min 5 s There is currently no option in MZmine to show retention time exactly the same way as Xcalibur does. I may add that option in next version. Regarding to your problems with peak detection, I need to know what parameters you used. When I set the parameters myself and tried peak detection on your file, I did not see any peaks below 120 m/z. Please send further replies to the [email protected], rather than to my address. Best regards, Tomas On Feb 18, 2011, at 10:26 PM, Blanz, Joachim wrote: > Dear Tomas, > > Thank you for your rapid reply. We have acquired a file especially for you > that shows the issue. > I included some screenshots as pdf file as well and included a question in > the pdf. > > Best regards, > > Joachim > > Joachim Blanz (PhD) > Investigator III > Novartis Pharma AG > Postfach > CH-4002 Basel > SWITZERLAND > > Phone +41 61 3240445 > Fax +41 61 3240342 > [email protected] > www.novartis.com > > > -----Original Message----- > From: Tomas Pluskal [mailto:[email protected]] > Sent: Donnerstag, 17. Februar 2011 02:35 > To: Developer discussion; Blanz, Joachim > Subject: Re: [Mzmine-devel] mzMine bug with retention time > > Hi Blanz, > >> I found that the retention times were wrong after having imported a Xcalibur >> rawdata file. I assumed that the number or >> time format could have influenced the display or calculation. However >> changing these settings according to the manual did not correct the >> retention time issue but made it even worse (was this implementation >> checked). Wrong assignment of RT is only in the seconds range but >> it already starts with the second scan. Did you assume constant scan rates >> or do you really read the actual retention time as it is stated in the >> rawfile scan by scan ? Could you please advise how to get the correct >> retention time as they are present in the rawfile. > > I am not aware of any problem like this. Can you send an example data file > and indicate where do you see the problem? > > >> >> Would it be possible to get the nearest MS/MS and MS3 mass spectrum included >> in the final table if the rawfile was acquired with data-dependent >> scanning ? This would help very much. Could you implement this feature or >> would it need additional action to get it implemented ? Please let me know >> what you think about implementing this special request. > > If you click right mouse button on a table row, you can choose "Show... > MS/MS" from the popup menu. This shows the most intense MS/MS scan with the > precursor mass equal to the peak you clicked on. > I hope this is what you were looking for. > > Best regards, > > Tomas > > > =============================================== > Tomas Pluskal > G0 Cell Unit, Okinawa Institute of Science and Technology > 1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan > TEL: +81-98-966-8684 > > <Original Xcalibur scans.pdf.zip><OrbTest_MDF.RAW.zip> =============================================== Tomas Pluskal G0 Cell Unit, Okinawa Institute of Science and Technology 1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan TEL: +81-98-966-8684 ------------------------------------------------------------------------------ The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb _______________________________________________ Mzmine-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mzmine-devel
