ppm reduction may be the reason for not getting all compound features in the result. When I run the same with 30 ppm I got Niacin, bit satisfactory. But how am I getting the K+ adduct in the result? Is it an impurity or a bug?
I have a good question for you and I really need your advice to proceed in XCMS online.
I have run the standards in XCMS online , which contain a mix of 9 compounds [attachment=1:2kl8ijyk]12_Compounds_mix.xlsx[/attachment:2kl8ijyk]. I have rum 4 mzXML file in each data set and customized the parameters for UPLC TOF.Please see the attachment for logarith [attachment=0:2kl8ijyk]Log _XCMSOnline version 1.docx[/attachment:2kl8ijyk]. Please see the result,[attachment=2:2kl8ijyk]Result_standard_poshilic.xlsx[/attachment:2kl8ijyk] I have sorted it based on intensities and removed the low intensity features for easy uploading in the forum, I got only five compound features matching with the standards run. I dont know where it went wrong. If the software is not running properly for the standards, which we know already,how will we use it for research. Please accept my apologies if I am wrong.
Could you please look into the data and let me know why I am not getting all the standards in the result. Also why I am getting K+ adducts if at all I didnt select it. Hope to hear from you soon Thanks alot,
Many thanks for the information. But my doubt is that if we do simple/ batch search there are many hits by Metlin for an m/z value(different combinations with the adducts selected, H+, NH4+, Na+ etc). As the process is called untargeted metabolyte profiling, how can I select the compound name for a feature from the listed metlin putative identifications. I think to get to know a way to insert a column for neutral mass of the compound will solve the issue, but how? I am completely depending XCMS/ XCMS online for my analysis, I may lose my project if I couldn't find an answer for this, as my mentor already have the compound name and neutral mass from a software Agilent Mass profiler Pro. I am reading the articles suggested by you.
With due respect for creating such a wonderful software I would like to thank you for the support. I really appreciate your help. I need to learn the basics of Metabolomics as I am from a public health background.
I would like to update that I found answer for first query, mz med value is with the adducts. But how to select one compound for a particular feature? Is OBIwarp is good for LCMS/ UPLC QTOF data?
I am using XCMS and metaXCMS as descibed in the protocol. But the issue is when I import three .tsv files from pairwise comparisons to meta XCMS (GTK+), I am getting the Venn diagram and excel with the common features. But I think it will be more user friendly if we get the compound name in the result. Could you please tell me how you will select the features and do METLIN search?
I am using XCMS online for processing and analysing a metabolomic data from UPLC - TOF (Agilent). I have downloaded the XCMS online package from bioconductor, also using R 2.15.2.
Somebody please tell me the best parameters for UPLC TOF [I have used general : retention time format - minutes, feature detection: ppm =10, min peak - 5, max peak - 20,retention time corretion: method - obiwarp,prof Step -1, alignment and statistics kept as default value,Annotation : search for - isotopes+adducts, ppm - 10, Identification: H+,NH4+,Na+]. Then I changed the retension time to seconds, when I checked the result for the cloud plot, It didnt show the feature points the plot.What will be the reason? I changed it into seconds as the limits are 5-20 seconds.
After analysing with this parameters for positive polarity, I met with some issues with diff report
Issue 1 - mz med value in diff report is the normal mass of the compound or with adducts? Issue 2 - The column METLIN in result.tsv shows many compound names for the same feature. Which one is appropriate to select or do you have any standard scoring system to pick one with max score. Issue 3 - What is the difference between obiwarp and peak groups.
My objective is to compare the XCMS online result with Mass profile Pro result.
The fast responses will be highly appreciated. Thank you, Sithara
if I couldn't find an answer for this, as my mentor already have the compound name and neutral mass from a software Agilent Mass profiler Pro. I am reading the articles suggested by you.