Hi, for sure Dr. Chris can help you better but I have tested your data and the problem is what I told you in the previous email. If your RT tolerance = 1, you have to decrease the parameter "min number of points" to 10. You can also increase a little bit the RT after correction. Also, the RT tolerance in Gap filling should be smaller if you are doing RT correction. The problems I see in the data are related with the peak detection and the gap filling. I left the project with the parameters I used in dropbox: https://dl.dropbox.com/u/45538644/deconvoluted.mzmine BR, Sandra
________________________________________ From: Raghavendra Gunnaiah [raghavendra.gunna...@mail.mcgill.ca] Sent: 19 July 2012 06:30 To: chris.pud...@syngenta.com Cc: mzmine-devel@lists.sourceforge.net Subject: [Mzmine-devel] In correct RANSAC alignment Dear Dr. Chris, I am not getting proper alignment of peaks across samples. Same peak within the set parameters (mz tolerance=0.01 or 5ppm and RT tolerance=1.0 min, RT after correction=0.5 min) appears in 2-3 rows. For example 145.0645 appears in 3 rows at 12.2 (detected in 3 samples out of 20), 12.46 (detected in 5), 12.52 (detected in 6 samples) which are within RT tolerance. In other samples, it is not detected after alignment but is present in all the 20 deconvoluted peak list and also in original raw files within the RT deviation. I don't understand about threshold value. When I give threshold value= RT tolerance (ex, 1.00 min in my case), I observe many of the peaks aligned as shown in the preview but I don't see such alignment in the aligned peak list. With threshold value <1.0 min, I don't see peak alignment in the preview also. My flow of work is as follows mzXML files import(20 files)>baseline correction>MASS detection(centroid) > chromatogram builder > deconvolution (wavelets_XCMS) >deisotoping and filtering > RANSAC alignment. I have also sent my files using dropsend for your reference I am using mzmine2 for metabolomics with LC-LTQ-Orbitrap at 60,000 resolution. Max RT deviation observed is <1.0 min. I tried with several parameters in permutation and combination but nothing worked. I am struck with this project since more than 15 days. I appreciate your early response with regards Raghavendra Gunnaiah Ph.D Scholar R1-013,Department of Plant Science McGill University Macdonald Campus 21,111 Lakeshore Road Ste. Anne de Bellevue, QC H9X 3V9 ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
