New features of MS-DIAL: 1. Modified IBF converter program to accurately calculate the decimal of ion mobility data's m/z values for accumulated MS1 spectra. 2. The normalization functions are now fully supported in ion mobility data processing. 3. Fixed the theoretical spectra of [M+Na]+ ion form of LPC and PC. 4. Fragment rule based lipid annotations were improved for several lipid subclasses especially in [M+Na]+ form. 5. Improved and fixed the programs from the feedback in MS-DIAL software forum.
I could reproduce the issue, and I fixed the program. (next week, I will upload the new version of MS-DIAL.) Meanwhile, please do not tick "Use reference spectrum to make MRMPROBS library" if your spectrum is "unknown". The program will try to use the reference (library) spectrum to generate MRMPROBS library file if it is ticked. If you do not tick it, MS-DIAL will use the experimental spectrum to generate the MRMPROBS library. Ane no error is occurred in the current version.
Thanks, this was the invalid file name characters issue due to "|" in the lipid metabolite name to be used as the file name of png and emf. I fixed it, and I will upload the latest version in next week actually. Thanks,
>>So I am thinking about setting A = 5,000 and B = 3,000. Does this sound like a reasonable approach for determining cut-offs?
These settings should be fantastic.
>>Concerning the ABF file converter, do you recommend selecting any of the options for my data? You do not have to change the setting. Please use the default setting for MSE data.
please follow the direction of Biswa. Also, the file of "GMD_20111121_VAR5_ALK_MSL.txt" in GOLM database website should be good to start to merge the library with the existing spectral records on my website.
as long as I understand your data, please follow the below setting. 1. Capture.PNG shows the example startup project window for your data. Note: SWATH-MS or conventional all-ions method is fine for your data actually. (although in fact you may use both methods) All-ions with multiple-CEs setting is actually made for the method incorporating three or more collision energies for all-ions like 0 SCAN 100 1500 MS1 6 1 1 ALL 100 1500 MS2 20 1 2 ALL 100 1500 MS2 50 1 3 ALL 100 1500 MS2 70 1 However, your data is obtained by two CEs setting. So the experimental file should contain the following information (as attached as experimental_file.txt).
ID MS type Start mz End mz 0 SCAN 100 1500 1 MSE 100 1500
The other columns like Name and CollisionEnergy are not used in "SWATH-MS or conventional all-ions" method option.
2. Use abf file format for your analysis actually. (I personally have never checked the process by mzML...) 3. I recommend to optimize (A) minimum peak height of peak detection tab (B) MS/MS abundance cut off of MS2Dec tab for your analysis to rapidly process your data. Especially check the baseline of noise signals. According to my experience for synapt g2 mse, the baseline of noise signal is around 10^5 - 10^6, and therefore, I used around 10^5 value for (A) and (B) parameters. If you use the default setting (1000 and zero for A and B), the processing time requires too much hours because it should also handle the noisy spectra.
Maybe, this kind of pie chart can be created by several idea/metadata. ion abundances, ion existences, etc... EnhancedGraphics is a good add-on on the cytoscape. And actually, you can export such a metadata (for example, ion existence) by Export-> Alignment result export -> Check "Peak ID". In the peak id matrix, the value will be negative if the peak is not detected in the sample, and the positive value of peak ID means the peak ID of each sample file.
about internal standard setting, please see: http://www.metabolomics-forum.com/index.php?topic=1406.0 Second, to modify the annotation result, one way is to use a "glass' button as attached. Or, for example, 1. open one alignment result. 2. on alignment spot viewer, click "show ion table" showing alignment table viewer. 3. here, you can modify the metabolite name by yourself. (but I recommend to put comments on comment column actually to keep the original annotation..
Finally, about the integration of pos/neg or completely different platform for pathway mapping. (sorry, there is no correlation analysis option in msdial)
1. as the condition, you have to import the same number of analysis files in each project. Then, you have to set the same "Class" name for the file group. Then, each project should have at least one alignment result. 2. Open one project. Then, open one alignment result file. 3. Go to Data visualization -> Pathway mapping 4. in lipidomics project, choose "metabolite name" as the key value, and in metabolomics project, please choose "inchikey" as the key value. 5. if you wanna import other project result, here, the program accepts max four additional project data. 6. Simply, click load button, then, choose "***.mtd2" project file of such the other project. 7. Then, choose one alignment result file. 8. After all project imported, please click Mapping. Then, you will find the result as attached.
sorry for this late reply. I was actually very sick last week... >>I would like to better understand how and where to set the information of the internal calibrants to make the normalization of chromatographic runs.
Sorry, I will remake the tutorial on my website soon, but currently, the "IS ID" column name was changed to "Target ID". So, 1. Go to Option->Alignment result property setting 2. Then, you will find the attached window. 3. Check the alignment spot ID of your internal standard. (If the alignment id of IS is 100,) Please add 100 on the cell of Target ID. 4. Right click on the Target ID column area-> Auto fill -> Then, all cells will be filled by 100. *You can easily set one internal standard like this, but if you have multi-ISs and if you wanna apply them to the independent peaks, you can do the similar things although it's a bit tough task... 5. Go to "Data visualization" -> Normalization -> Internal standard-> Done 6. Then, all your data will be normalized. 7. The normalized data can be exported from Export -> Alignment result export -> check "Normalized".
>> would also like to understand what they are and how to use the parameters that show ion table and specifically Fill and Correlation
"Correlation" see: http://www.metabolomics-forum.com/index.php?topic=1385.0 Correlation is very simple function where the correlation of ion abundances among samples are calculated between aligned spots, then, you can check the aligned spots having similar metabolic profiles there.
thank you very much for this suggestions! Yes, I will definitely address this issue in the next update. Since I will post the updated version on the mid of Feb, I will send you the evaluation version of MS-DIAL to ask if it works for you or not.
yes, it's true. Sorry, probably, all users will be able to know what ms-dial does in the program for lipid annotations once I can reach to the publication of MS-DIAL 4 paper. All algorithms are there actually. I hope, it will be published in this summer...
Simply: the current MS-DIAL program performs a "hybrid" annotation system including (1) a classical similarity matching (dot-product and reverse dot product) algorithm (2) a rule-based decision tree algorithm to describe an appropriate structure representation of lipids by considering the mass fragment ions.
Now, the MSP file records are actually used for the first purpose (dot-product and reverse-dot product). And the spectrum similarity score is used to filter out the noisy spectra. Currently, in lipidomics project, if the dot product score is less than 0.1 AND the reverse dot product score is less than 0.5, the spectrum is recognized as "Unknown" at this stage. Then, the mass fragment ions are evaluated by the decision tree program. In the ether PE case, the experimental spectrum is evaluated to judge if it's from plasmanyl type- or plasmenyl type. Then, if the spectrum was estimated as "plasmenyl (plasmalogen) type", the representation is changed from PE O-XX:X_YY:Y to PE P-XX:X-1_YY:Y.
