as you can read it here (http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL/index3.html), the fill % means the "gap-filled" sample % (but 1 means 100% in the output). If you analyzed 10 samples, and if a metabolite is detected in eight samples of them, the fill % value becomes 0.8.
However, the S/N value is re-calculated in the gap-filling process. If you wanna check "which samples really contain that component", I recommend like this:
(after opened an alignment result in MS-DIAL) 1. Go to "EIC of aligned spot" tab (top panel of MS-DIAL). 2. Right click, and click "Table viewer for curating each chromatogram" 3. Here, you can check which sample has the component in the "Annotation" column.
Does it make sense for you? Please let me know if it's helpful for you or not.
It makes sense for me. Of course, using the option of "identification after alignment" is good when you have many samples and many reference records.... However, I recommend to do the identification process for all samples. I think, the result of peak alignment becomes better by this because the representative spectrum can be retrieved from a spot having a good match with the reference spectrum.
If you wanna get all of required information with a good computational skill, "mztab-M" format export should be a great option to retrieve the standardized metadata (available from version 4.10).
--can we export a * .MGF file and a peaktable * .csv or * .txt using spectra from the "MS2 acquired" filter? Sorry, there is no function yet. It should be in the to-do list for the future development.
currently, there is no way to generate such an "order-made" retention time library for lipidomics project. (if you wanna use the retention time information, you should follow the same LC condition that I have provided.) Recently, our team is developing the utility to replace the retention time information by importing the user-defined training set including the pairs of retention time and SMILES codes. So I will post the news when it's ready for end-users.
MS-DIAL will recognize the following field names for retention index information in MSP. RETENTIONINDEX: ** Retention_index: ** RI: ** (Ignore case)
Unfortunately, (probably), lib2nist will convert nist_ri library to msp with the retention index field like Synon: UN 1661 (Related) , and the information will not be retrieved in MS-DIAL program. And as you mentioned, nist_ri and several information of nist14/17 will have several retention index information from several column types.
I am using PaDEL or CDK to generate the compound descriptors, and recently, xgboost, random forest, ksvm etc can easily be used to make a model for RI predictions in R etc.
thanks Biswa, yes, it's true for 'metabolomics' project of MS-DIAL, and adding the user-defined spectra in lipidomics are a bit tricky.
MS-DIAL lipidomics project currently utilizes the LBM2 binary format which serializes the ASCII MSP format (1) to reduce the file size for rapid retrieving the library file (if the file is formatted by ASCII, the current file size exceeds 1GB actually), and (2) to keep the contents private till publications.
However, MS-DIAL itself can also import the previous "LBM" ASCII format file in lipidomics project. I uploaded the publicly available LBM spectral information in the following section that Biswa introduced. http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL/index.html
LipidBlast fork (Last edited in January 2th, 2020) ASCII file (lbm) for MS-DIAL lipidomics (ajusted Oliver Fiehn lab LC-MS method): Download
Please note that the LBM file does not contain the full information of LBM2, the content information of public-LBM is mostly "one third" of LBM2. Sorry, but this is actually important to keep our priority in the lipidomics research field. (I will open the full spectra after I publish our latest paper.) BTW, the content of LBM2 is summarized in http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL/index5.html. *Note that not all of lipid subclasses described in the above page can be utilized in MS-DIAL. I will open them when my latest paper is opened.
I summarize the process for how to modify the LBM format file and how to use it in the lipidomics project. 1. please exclude the original LBM2 format from the MS-DIAL folder. (The program accepts only one LBM/LBM2 file in MS-DIAL folder.) 2. open the LBM file by a text editor like wordpad/notepad++ (but the public-LBM file has already been very big, the file may not be opened by notepad++. In such case, you have to use UNIX command etc.. 3. Please paste your own spectral records to the LBM file with the "COMPOUNDCLASS: Others" field. *If you put the "Others" term in the CompoundClass field, it can automatically import all of your queries. It means that you can simply add the MSP-formated ASCII records in the lbm file. For the records containing "COMPOUNDCLASS: Others", the classical spectral matching algorithm using dot-product, reverse-dot product, and fragment presence percentage is used for the annotation although the lipidomics project basically uses a hybrid scoring method using such the classical similarity algorithm and a decision tree algorithm to represent the suitable lipid structure information based on the characteristic fragment existences. 4. Please save it. Then, you can use your customized spectral records in the lipidomics project.
BTW, you can check the contents of the public-LBM file by UNIX command like: For checking lipid subclasses included: grep "COMPOUNDCLASS: " **.lbm | sort | uniq For checking all lipid species included: grep "NAME: " **.lbm
Question: With issues such as 'version control' / 'versioning' how does one keep track of various versions and their capabilities or say, changes?
I am posting the news in the "New Features and Changes" of the following website. http://prime.psc.riken.jp/Metabolomics_Software/ If you go to the "change log", you can check all the history logs for msdial, msfinder, and mrmprobs etc.
Also, in the MS-DIAL program, if you export the parameter setting file from Export -> Alignment result exort -> Check "Parameter": Here, you can find the version number of MS-DIAL to know which MS-DIAL version was used to generate the alignment result.
Also, from 4.10, I also made a history tracking function in MS-DIAL to parse (1) if users changed the annotation (from search function) or not (2) if users modified the peak integrations (from aligned EIC chromatogram tab) or not. You can find the information in the alignment result file.
->Qizhi
CAS...in principle, of course yes, but if I make such information, I will provide more database ID information including HMDB, KEGG etc as also described in my msfinder project. I will try to provide such a database information in the MS-DIAL project window. Meanwhile, of course, you can use PubChem identifier exchange service: https://pubchem.ncbi.nlm.nih.gov/idexchange/idexchange.cgi CTS: http://cts.fiehnlab.ucdavis.edu/ for your purpose.
(below is also true in LC-MS/MS project.) the representative spectrum is retrieved from one of the analysis files as follows. 1. the spectrum will be retrieved from a sample having the highest score of EI-MS spectral matching with a reference spectrum. 2. if there is no annotated information among samples, the spectrum will be retrieved from a sample having the highest peak height (by the defined quant mass in GC-MS project) among samples.
Can you find a good spectrum in each file? If you find a good spectrum in each file but if you cannot find any good spectrum in the same/similar retention time area, there is a possibility that the alignment spot having such a good matched can be excluded in the finalization process as discussed in the below chat. http://www.metabolomics-forum.com/index.php?topic=1391.msg4084#msg4084
(in such case, the issue may be resolved if you can define the quant mass field that does not share co-eluting metabolites each other.)
If you cannot find any good spectrum in any result file (in peak viewer), please send me a netcdf or abf file to check the issue.
Hi, I reactivated the method in today's update. However, I am not sure if this function works or not right now. Actually, I could not validate the function on my side because I did not have an account for MoNA. Although I tried to register in MoNA server, it gives me an error for making my account. I am now asking Gert and Diego of UC Davis, and they will provide their answers in new year, so please wait a bit. Hiroshi
thanks, I actually checked my source codes, and I could resolve this issue. 1. please download the latest version at http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL/index2.html. 2. The high resolution's quant mass should always be displayed if you do not use "Use quant masses defined in MSP format file". 3. If you use the option of "Use quant masses defined in MSP format file", the quant mass becomes nominal if the record has Quant mass field by nominal mass.
Also, as you find, the option "Use quant masses defined in MSP format file" will affect the alignment result. MS-DIAL provides the two dimensional alignment spots (RT vs Quant mass) as the result of peak alignment, but in the data processing, the alignment spots which have very similar RT and Quant mass values will be finalized so that one representative alignment spot is stored. Namely, if there were three spots having such similar RT and Quant mass values, two of them will be erased in the alignment process. Therefore, if your MSP file has many same quant mass values, the possibility to exclude alignment spots becomes higher than the case that you have set different quant mass value for each metabolite.
About: (2) Yes, all from your RIKEN website, plus in house libraries. I see that the exact masses (see attached picture of 2 examples from EI-B and Fiehn-EI spectra) that in deed the masses are nominal mass, and the Exact Mass is several decimal places.
See attached picture. The MSP files on my website will have "QUANTMASS:" field that is used for quantifying the metabolite by the quant mass value +/- user-defined mass accuracy if you ticked the option of "Use quant masses defined in MSP format file". I hope, your problem is resolved if you do not use this option actually. Or, you may replace the quant mass field with an accurate mass by your definition although it's not easy actually...
1. It seems that we can only export all alignment peaks but not filtered results except for the blank subtraction. For example, sometimes, I only want to export those "annotated" results or only those most intensive peaks but not all. 2. Can we export alignment results from the alignment table after applying for example comment filter?
-> For these two questions, there is no function for these yet. And I should put them on our to do list.
3. Some entries in my library do not have RI information, but I use RI for scoring for the identification, is it possible that a candidate with a very high spectral match will get a very low score because of the lack of RI information?
-> If you check "Use RT/RI for scoring" for the identification process while there is no RI information or the RI field has negative value (like -1), only EI-MS similarity score is used as the total score. On the other hand, if there is an RI information, the total score is calculated by integrating RI/RT similarity and EI-MS similarity scores like:
public static double GetTotalSimilarity(double rtSimilarity, double eiSimilarity, bool isUseRT) { if (rtSimilarity < 0 || !isUseRT) // isUseRT is true when use RI/RT information for scoring is checked { return eiSimilarity; } else { return (0.6 * eiSimilarity + 0.4 * rtSimilarity); } }
4. My problem is that the Alignment ID in the exported text, e.g. signal to noise information, is different from that in the MSP file. Exported texts keep original Alignment ID obtained in the MS-DIAL alignment process, while MSP creates new Alignment ID when exporting MSP file.
-> sorry, I fixed the issue in my source code. And you can find those meta data information in the exported MSP from the next version.
the scan number that you find in ms-dial does not have the same meaning as in mzmine. I have an idea. Did you start your project as "profile" mode in the start up window of MS-DIAL? or did you start it as "centroid" mode? If you start with "profile mode" for both ms1 and ms/ms, can you try to restart your project by selecting "centroid" for both ms1 and ms2?
msdial has already exported retention time and retention index fields as well, but nist ms search program did not recognize the files. I learned the field definition from https://www.nist.gov/system/files/documents/srd/NIST1aVer22Man.pdf, then, I modified the exporter. Here, you can see retention time and retention index in comment field, and maybe, the retention index is used for searching candidates in nist ms search program.
