Hi Jamuna, A few points:
1) The strange TIC plot is caused by merging scans of two different functions. If you "unroll" your data file "Sept 22 Ref 7.mzXML", you will see it contains profile scans #1 to #8991, and centroid scans #8992 to #9093. At this point MZmine cannot separate these two functions, but I will work on that. [image: Inline image 3] 2) As for detection of two 166 m/z peaks, I got only one using the parameters you provided.[image: Inline image 2]. Did you use the centroid mass detector? If yes, that could be the cause of the problem. Use the Exact mass detector. 3) I added a few comments to your parameters.doc (attached) 4) Just a note: MZmine 2.13 can now import Waters RAW data directly, no conversion to mzXML by msconvert is necessary 5) Next time you can send a single MZmine project file, it will save my time :) Best regards, Tomas On Sat, Feb 7, 2015 at 1:30 AM, jamuna risal <jri...@gmail.com> wrote: > Dear Tomas, > > Thank you very much for a quick response. here, I am sending you the > data files. > > I have uploaded the file in google drive and shared the file. I hope you > will be able to look at this. > > > https://drive.google.com/folderview?id=0Bz183RKCUevxRW9EdmVhejZIaDQ&usp=sharing > > > Since, I am new to this software and already sending you the data files, > may I also take this opportunity to ask you further about the parameters? I > am closely looking at the peak 166.02, which is phenylalanine (monoisotopic > mass: 165.07898). With the parameters i gave (attached along with data) > leads to two separate peaks during peak alignment. Since this is a > reference sample, i am not expecting two peaks at 4 min. is it possible > that I have to relax m/z and/or RT tolerance during processing? > > Thank you and apologize for taking your time. > > jam > > On Fri, Feb 6, 2015 at 12:26 AM, Tomas Pluskal <plus...@oist.jp> wrote: > >> Hi Jamuna, >> >> I think you don’t need to worry about the R warnings in the console. >> These should be harmless. >> >> However, I notice the TIC visualizer shows a strange line in the >> chromatogram plot of your data. Could you perhaps send us a sample data >> file, so we can debug this problem? >> >> Tomas >> >> >> >> On Feb 6, 2015, at 04:01, jamuna risal <jri...@gmail.com> wrote: >> >> I am running MzMine 2.12 in 64 bit Win OS. java version 8 and R-3.1.2 >> in 64 bit. >> I have not changed heap size but slightly adjusted the R_Home >> in startMzMine script. >> >> I converted .RAW data to MzXML format using msConvert of the >> proteoWizard. After importing raw file, I did crop filter and then started >> the baseline correction using peakdetection baseline corrector (Parameters: >> TIC, m/z bin width of 0.5 and no. of scans left and right 20, and lwin and >> rwin 5 and multiplier 1). There is a R- error message, however, at the end >> it says baseline corrected and I can see that in the chromatogram also. >> >> If somebody can suggest me what is the error and what is it doing or >> not doing for the baseline correction, I would really appreciate the >> response. >> >> Thanks. >> >> jam >> >> >> >> -- >> Jamuna Risal Paudel >> <Baseline.PNG><command.PNG> >> ------------------------------------------------------------------------------ >> Dive into the World of Parallel Programming. The Go Parallel Website, >> sponsored by Intel and developed in partnership with Slashdot Media, is >> your >> hub for all things parallel software development, from weekly thought >> leadership blogs to news, videos, case studies, tutorials and more. Take a >> look and join the conversation now. >> http://goparallel.sourceforge.net/_______________________________________________ >> Mzmine-devel mailing list >> Mzmine-devel@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/mzmine-devel >> >> >> =============================================== >> Tomas Pluskal >> G0 Cell Unit, Okinawa Institute of Science and Technology Graduate >> University >> 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan >> WWW: https://groups.oist.jp/g0 >> TEL: +81-98-966-8684 >> Fax: +81-98-966-2890 >> >> > > > -- > Jamuna Risal Paudel >
Parameters.docx
Description: MS-Word 2007 document
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