CAROLINA GONZALEZ: we use an extraction method for multiplataform analyses. We add MeOH:H2O 50% (1mg tissue:10uL solvent) for Mouse face Brain homogenization using a TissueLyser. Then, we mix 100uL of brain homogenate with 320uL MeOH + 80uL MTBE (for lipids) DOI: 10.1021/acs.jproteome.8b00816.
WENYUN LU: For tissue samples our preferred extraction method is first grind into powder then add 40:40:20 methanol:acetonitrile:h2o+0.5% formic acid then neutralize with 15% NH4 HCO3 followed by two rounds of centrifugation. https://doi.org/10.1089/ars.2017.7014
Feel free to follow up with further Qs here or there!
Last post by gregopim -
Hello everyone, By any chance, does anyone have found a way to import the HMDB spectra library in Progenesis? Progenesis only support .msp files for spectra libraries, but HMDB only provides .xml or .txt versions (https://hmdb.ca/downloads). Is there a way to convert .xml files to .msp? Grégory
I did all my samples data processing following the exact parameters you gave me, but I still have problems with my IS: - One of my IS is still not found by MS-DIAL (one of those that were missing previously) - The other detected by MS-DIAL, which is better. But the identification using a .txt file as in-house library did not work, and the feature in the ion table present a high mass deviation compared to my IS mass (approx 13 ppm instead of < 5 ppm when I am checking with XCalibur).
One of the group I am processing a few samples were not spiked with the IS(3 vs 28 samples spiked). Do you think it can be related (even if it should not)?
I just checked your positive ion mode data. It works fine. Of course, several IS compounds were not detected owing to the structure property. However, at least, I could detect the peaks that you wrote as "Not detected by MS DIAL in ESI pos" in the excel.
I also pasted the parameters that I used. Thanks,
Hiroshi MS-DIAL ver. 4.60-dev
#Project MS1 Data type Profile MS2 Data type Profile Ion mode Positive Target Metablomics Mode ddMSMS
#Data collection parameters Retention time begin 0 Retention time end 100 Mass range begin 0 Mass range end 2000 MS2 mass range begin 0 MS2 mass range end 2000
#Peak spotting parameters Mass slice width 0.1 Exclusion mass list (mass & tolerance)
#Deconvolution parameters Sigma window value 0.5 MS2Dec amplitude cut off 0 Exclude after precursor True Keep isotope until 0.5 Keep original precursor isotopes False
#MSP file and MS/MS identification setting MSP file Retention time tolerance 100 Accurate mass tolerance (MS1) 0.01 Accurate mass tolerance (MS2) 0.05 Identification score cut off 80 Using retention time for scoring False Using retention time for filtering False
#Text file and post identification (retention time and accurate mass based) setting Text file E:\0_SourceCode\BugReports\20210414_GrosFich\pos_mzrt_lib.txt Retention time tolerance 0.5 Accurate mass tolerance 0.01 Identification score cut off 85
#Advanced setting for identification Relative abundance cut off 0 Top candidate report False
#Adduct ion setting [M+H]+
#Alignment parameters setting Reference file E:\0_SourceCode\BugReports\20210414_GrosFich\210322_SWS_QC4_ESIpos_14.raw Retention time tolerance 0.05 MS1 tolerance 0.015 Retention time factor 0.5 MS1 factor 0.5 Peak count filter 0 N% detected in at least one group 0 Remove feature based on peak height fold-change False 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 Gap filling by compulsion True
#Tracking of isotope labels Tracking of isotopic labels FALSE
I have a question about using MSDial to analyze the Agilent 6560 ion mobility AIF data. For example, in attached picture 1, when I select chromatography as the separation type, "SWATH-MS" and "All ion with multiple CES" option are available in the MS Method type.
However, in attached picture 2, when I select the "Ion mobility" in the separation type, there is no option about "all ion with multiple CES"
Thus, I am wondering how to use the MSDial to analyze the data which run under ion mobility and AIF using Agilent 6560.
Last post by capkavl -
Thank you Hiroshi. The error is the same if I select raw heights as an output combined with mztab-M. If this could be looked into for the next version it would be great. Thank you, Vladimir.
Here is a link to download two of my .raw data and an excel file with the information you requested. I have the same problem in ESI negative, but with more IS not picked up by MS DIAL (7/24 not found), so I attached a .raw file in both modes: grosfi.ch/adm4hAq6bpD