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CAMERA / Re: Feature selection for downstream statistics
Last post by Wang -Thanks.
Thanks.
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Sample preparation / Re: Mice brain preparation for HPLC
Last post by Alexandra -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!
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Other / Progenesis QI and HMDB spectra
Last post by gregopim -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
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MS-DIAL / Re: Not all my internal standards are detected
Last post by BBonnefille -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)?
Thank you for your help,
Bénilde
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MS-DIAL / Re: Not all my internal standards are detected
Last post by BBonnefille -Thanks a lot, I will make a new try using the parameters you used.
Bénilde
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MS-DIAL / Re: Not all my internal standards are detected
Last post by Hiroshi Tsugawa -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
#Centroid parameters
MS1 tolerance 0.01
MS2 tolerance 0.025
#Isotope recognition
Maximum charged number 2
#Data processing
Number of threads 1
#Peak detection parameters
Smoothing method LinearWeightedMovingAverage
Smoothing level 3
Minimum peak width 5
Minimum peak height 10000
#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
#Ion mobility
Ion mobility data FALSE
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MS-DIAL / How to analyze Agilent 6560 ion mobility AIF data?
Last post by kljw001 -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.
Thanks a lot
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MS-DIAL / Re: How to export alignment result in mztab-M format
Last post by capkavl -Thank you,
Vladimir.
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MS-DIAL / Re: Not all my internal standards are detected
Last post by BBonnefille -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
Thank you for your help,
Bénilde
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