Hi Tomas I think that we should use these names to follow the IUPAC recommendations: - Total ion current (or TIC) [= what you refer to as TICsum] - Base peak chromatogram [= what you refer to as TICmax]
I don't like TICsum and TICmax since these are not standard terms and therefore will confuse the users. As for the XIC, then I agree that we have to be able to account for the plot type (base peak intensity or total ion current). I suggest that we use the following terminology to make it as clear as possible: XIC - Total ion current XIC - Base peak intensity But if you would rather that we use short names like XICsum and XICmax [or XIC (Sum) and XIC (Max) ] then let's go for that but then I suggest that we add (Sum) and (Max) to the plot type names in the parameters. I cannot find a standard definition of how to distinguish the two XIC plots and I actually think that many people don't realise that an XIC plot can be generated in two different ways. Cheers, Thomas -----Original Message----- From: Tomas Pluskal [mailto:plus...@oist.jp] Sent: 26. februar 2015 06:19 To: Developer discussion Subject: Re: [Mzmine-devel] Questions about the XIC plots Hi Thomas, > Sorry for my late response. I do think that the plot should be labelled "XIC" > and not "Base peak plot". The way I read the IUPAC Recommendations > (http://www.iupac.org/home/projects/project-db/project-details.html?tx_wfqbe_pi1%5bproject_nr%5d=2003-056-2-500) > (PDF can be found here: > http://pac.iupac.org/publications/pac/pdf/2013/pdf/8507x1515.pdf) a base peak > plot shows the intensity of the maximum intense peak in each spectrum over > the retention time and therefore shows data from many m/z measurements > whereas an XIC plot shows only the intensity of a narrow range of m/z values > over the retention time. Ok, I agree that according to the IUPAC recommendations we should not call it "Base peak plot", because they only define base peak relative to the whole spectrum. However, we still should somehow distinguish the two types of plot that we have: sum and max. Remember, each chromatogram plots some m/z range (TIC plots show the whole m/z range, while XIC plots show a selected narrow sub-range). Within this given range, we can plot either sum of all intensities (that's what MZmine now calls TIC) or a maximum intensity (that's what MZmine now calls Base peak). We could distinguish these by making 4 types: TICsum TICmax XICsum XICmax Or, any other idea? Tomas =============================================== 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 ------------------------------------------------------------------------------ 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 ------------------------------------------------------------------------------ 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
