sounds like the alignment is too strikt with the accurate mass.
I dont have access to an accurate gc-ms, but I know that the alignment settings can be changed for accurate mass for lc-ms but there is no mass deviation setting for normal gc-ms. Maybe its missing for accurate gc mass or hidden in the tab where you can click accurate mass (peak detection)?
at the moment I have small sets of samples (around 100 per experiment).
The problem I am facing with all my different experiments is after I close the Table viewer for the aligned chromatograms, the program crashes about 20% of the time. I have the feeling, the longer I am in the table viewer, the higher the chances are.
Is there a logfile or a debugging mode I can view/switch on?
Thank you, all the best,
Martin
Language: English (UK) Windows 10 Pro
MS-DIAL ver. 4.60
#Data type Data type Centroid Ion mode Positive Accuracy type IsNominal #Data collection parameters Retention time begin 0 Retention time end 45 Mass range begin 50 Mass range end 600
#Data processing Number of threads 4
#Peak detection parameters Smoothing method LinearWeightedMovingAverage Smoothing level 3 Average peak width 20 Minimum peak height 1000 Mass slice width 0.5 Mass accuracy 0.5
#MS1Dec parameters Sigma window value 0.5 Amplitude cut off 10
#identification MSP file F:\Biology\Libraries\GCMS DB_FiehnBinbase-KovatRI-VS2.msp RI index file see last Retention type RI RI compound Alkanes Retention time tolerance 0.5 Retention index tolerance 25 EI similarity library tolerance 70 Identification score cut off 70 Use retention information for scoring True Use retention information for filtering False Use quant masses defined in MSP format file True
#Alignment parameters setting Reference file F:\Biology\Data\2021_Macro_ExpII_IntSt-MB\BT TOF\mzml\abf\Pool_1_b1_SL_start_275sec.abf Retention time RI Retention index tolerance 20 Retention time tolerance 0.075 EI similarity tolerance 70 Retention time factor 0.5 EI similarity factor 0.5 Identification after alignment False Gap filling by compulsion True Basepeak mz selected as the representative quant mass False
#Filtering setting Peak count filter 0 N% detected in at least one group 0 Remove feature based on peak height fold-change True Sample max / blank average 5 Sample average / blank average 5 Keep identified and annotated metabolites True Keep removable features and assign the tag for checking True
I have a question concerning the Retention Time and Index in MS-Dial compared to ChromaTOF:
I process Leco BT-TOF accurate GC-MS data. For testing I loaded 5 Quality Controls with increasing concentration. The Peaks are found, integrated and aligned really nicely!
But when I check the peaks in ChromaTOF I dont find any of them at those times. So I looked for my Internal Standard, and when I have a look at the EIC in my blank, there is one nice peak with 361 at 16.7 minutes (the Internal Standard). Yet when I check the time for the peak in ChromaTOF it says 1250 seconds, which would translate to 20.833 minutes.
When I have a look at the Retention Index it says 1890 in MS-Dial, and 2292 in Chromatof, calculated with the same Kovats-RI List.
The files were directly exportet as mzml in centroid mode from Chromatof and then transformed to abf. No Retention Time cutting was performed.
I hope my question is somehow clear and somebody has an Idea what setting I chose wrongly!
