Peak intensity not registered for all samples May 25, 2021, 12:41:04 AM Hello Hiroshi,Thanks so much for developing MS-dial, it is such a great program!I am currently analysing metabolomics data using version 4.6. After processing the raw data and scrolling through the ion table I opened up the chromatogram and visualised the individual peaks for each sample. I noticed that lots of those samples had a peak intensity of 0, despite there being a clear clean peak there (right top table, picture 1). I learned then that I can manually modify those peaks by following what is indicated on the left table (picture 1). So after updating I then got an intensity for all peaks (picture 2). I was wondering:- Why are so many peaks not detected and assigned an intensity of 0? I unticked the gap-filling option so I wondered if this was the reason?- If that was not the reason, should I perform this manual adjustment for all metabolites detected? Prior to this I would replace all values by 1/10 of the minimum peak intensity during the export option. However, I can really see how this could bias my results, especially when that 1/10 assigned would not approximate the actual intensity of those peaks. On the other side, I could never manually change all of them as I detected over 19'000, so if I only did it for a subset of more interesting ones, I would also be biasing my final result. What do you suggest?I couldn't find any reference to this functionality on the tutorial page, so I wanted to check directly with you.Thanks in advance for your input.Giulia. Quote Selected
Re: Peak intensity not registered for all samples Reply #1 – May 25, 2021, 03:15:40 PM Could you please provide some detail about your parameter setting, e.g., peak detection and alignment tab. Best, Sukis Quote Selected
Re: Peak intensity not registered for all samples Reply #2 – May 25, 2021, 04:47:56 PM Hi Sukis, sure, below are all of the parameters I used. Same both for positive and negative mode. Thanks!MS-DIAL ver. 4.60#ProjectMS1 Data type ProfileMS2 Data type ProfileIon mode NegativeTarget MetablomicsMode ddMSMS#Data collection parametersRetention time begin 0Retention time end 32Mass range begin 50Mass range end 1000MS2 mass range begin 50MS2 mass range end 1000#Centroid parametersMS1 tolerance 0.002MS2 tolerance 0.002#Isotope recognitionMaximum charged number 2#Data processingNumber of threads 2#Peak detection parametersSmoothing method LinearWeightedMovingAverageSmoothing level 3Minimum peak width 5Minimum peak height 100000#Peak spotting parametersMass slice width 0.05Exclusion mass list (mass & tolerance)#Deconvolution parametersSigma window value 0.5MS2Dec amplitude cut off 0Exclude after precursor TrueKeep isotope until 0.5Keep original precursor isotopes False#MSP file and MS/MS identification settingMSP file E:\Metabolomics\Database\MSMS-Neg-MassBank.mspRetention time tolerance 0.1Accurate mass tolerance (MS1) 0.002Accurate mass tolerance (MS2) 0.002Identification score cut off 80Using retention time for scoring FalseUsing retention time for filtering False#Text file and post identification (retention time and accurate mass based) settingText file E:\Metabolomics\Database\Edited_STd.txtRetention time tolerance 0.1Accurate mass tolerance 0.002Identification score cut off 85#Advanced setting for identificationRelative abundance cut off 0Top candidate report True#Adduct ion setting[M-H]-[M+Na-2H]-[M+Cl]-#Alignment parameters settingReference file E:\Metabolomics\MSDial abf converted data\28-QC_2.abfRetention time tolerance 0.1MS1 tolerance 0.003Retention time factor 0.5MS1 factor 0.5Peak count filter 0N% detected in at least one group 0Remove feature based on peak height fold-change TrueSample max / blank average 5Sample average / blank average 5Keep identified and annotated metabolites FalseKeep removable features and assign the tag for checking FalseGap filling by compulsion False#Tracking of isotope labelsTracking of isotopic labels FALSE#Ion mobilityIon mobility data FALSE Quote Selected
Re: Peak intensity not registered for all samples Reply #3 – June 08, 2021, 01:33:39 PM Hi Giacono,Is it possible that you have too small MS1 tolerance for alignment?Best, Sukis Quote Selected
Re: Peak intensity not registered for all samples Reply #4 – June 27, 2021, 03:37:42 AM Hi Giacono,>> I unticked the gap-filling option so I wondered if this was the reason?Yes, this is the reason. Did you try the processing with the gap-filling option?Hiroshi Quote Selected