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Messages - drchrispook

16
MS-DIAL / Re: Batch alignment in MS-DIAL 4.92
MS-DIAL automatically aligns all extracted peaks. I don't think the batch information is taken into account in that process. You have to set the RT window in the alignment tab high enough to catch any RT drift from batch to batch and then it will recognise those peaks as the same feature. If not you will get multiple features with the peaks split between them. My students have tried various RT windows up to about 0.5 mins, dpending on how bad their batch effects are. The problem here is when you have isomeric pairs and the alignment mismatches them. There's no perfect solution so you have to accept some compromises. If you want to get the most out of the data you have to go through your entire data set peak-by-peak to correct dodgy alignments and integrations.

I would be careful with RT correction. I have found it introduces artifacts.
http://www.metabolomics-forum.com/index.php?topic=1900.0
17
MS-DIAL / Re: RT correction
Yeah, I don't like this. Instead I've worked out that converting your data to mzML means you can just add an RT shift to the time value of each scan. I've just done a fixed shift but if I spend a couple more hours sampling different shifts between my batches I could use a function to correct it instead. 
18
MS-DIAL / RT correction
Has anyone used RT correction successfully? I can see that it works to align the shifted peaks from my two batches of analysis (see RT_correction screenshot) but the peaks are distorted. See other pics for examples. Won't this affect quantification?
I'm running v4.9.221218
Thanks,
 Chris
19
MS-DIAL / MS-DIAL v4.92 lipid ontologies are incorrect
In case anyone else is relying on these for filtering their data, lysophosphatidylcholines are being classified as HexCer_NDS and phosphatdylchlines as OxTG. These are obviously incorrect. I haven't tested this in any other versions.
20
MS-DIAL / Re: MS-DIAL and MS-FINDER library limits
Tsugawa Hakase, kon'nichiwa.

Thank you for your response. I have spent quite some time working with MS-FINDER since you posted this response. I hoped to have worked out a solution myself but I am afraid I still do not understand how the software works to calculate match factors. I am not familiar with the C language so, while I had a quick look at the source code as you suggested, I could not easily identify the code where the spectral matching is carried out. 

I am still rather confused as to how MS-FINDER calculates spectral similarity. Is it a pure dot product score in the Structure Finder results window? Or is it weighted DP, or reverse DP? I am also confused as to how to get custom spectral libraries to produce consistent results in MS-FINDER. If I load the custom library I use for MS-DIAL I don't get any annotations from the Structure Finder. Instead I appended the contents of that file to the internal library file, MS-FINDER ver. 3.52 Windows\Resources\MSMS-DBs-vs1.etm The program now produces matches but these differ subtly from those assigned by MS-DIAL. Can you confirm whether the two programs use different versions of the dot product?

21
MS-DIAL / msp export of DDA data for MS-FINDER doesn't contain MS1 spectrum
Hi, the export function for .msp in v4.80 doesn't write the MS1 spectrum to the file. See attached screenshot of example data. I think this is important for formula inference. The MS1 spectrum is present in the alignment export though so the information just isn't being written.
Regards,
Chris


EDIT 5 minutes later: This is my error. If you want the MS1 spectrum as well as MS2 then you can't export to .msp format because it only holds a single spectrum. Export in .mat format instead using the "Export" button instead of the "Save as MSP" button. See highlight in my second image.
24
MS-DIAL / Re: Merge MS Dial exported outputs
Hello Cristina,
if you load each alignment to a dataframe you can use the biggest as a reference. You can iterate over the others row-by-row and test each mz/rt pair for matches against every feature in the reference. When you obtain matches you could aggregate peak areas from both dfs in a new dataframe. This is fairly straightforward in Python.
Chris
27
MS-DIAL / Re: MS-DIAL and MS-FINDER library limits
Further to previous, I have duplicated the inconsistent matching for positive control spectra with a couple of other subsets of my NIST .msp library. Setting the match factor threshold very low, as Biswa advised, helps to produce good results. With the threshold at the default of 80% I didn't get matches for my positive control, even when that exact spectrum was in the library. When I lowered it to 5% I got matches, including the same spectrum scored at 100%. So there seems to be a bug with the way MS-FINDER returns database hits. I have attached the files to reproduce this.
28
MS-DIAL / Re: MS-DIAL and MS-FINDER library limits
Hi Biswapriya,

thanks for your response. Good to know that there's no limits to this brilliant software! I've run the same tests as you and it seems to work fine. I've also imported a subset of the subset as query spectra into MS-FINDER as a sanity check and it does a pretty good job matching them up. Not perfect though, which is worrying. For example, searching a series of query spectra for PC(16:0, 18:2) across varying collision energies I get five spectral matches returned from the library for query CE of 14, none for CE16 and seven for CE20. Visually inspecting the CE16 spectra there is little difference between that and adjacent CE spectra, as you would expect. So I don't understand why I get no matches. It would be great to have a variety of matching algorithms, as are available in MS-DIAL (dot product, reverse dot product, unweighted dot product, presence peak score, total MS/MS similarity score). I can't see where to vary the match factor threshold in MS-FINDER either and I can't tell what the algorithm its using is.

Do you use your own scheme for .msp keys? I am thinking I will edit the libraries to remove fields that the software doesn't use, in case those are the problem.
Cheers,
 Chris
29
MS-DIAL / MS-DIAL and MS-FINDER library limits
Hello,

I have converted the 2020 NIST HR-MSMS library to .msp format and tried using it in MS-DIAL and MS-FINDER. I had to amend some keys as the NIST ones didn't match that of the MS-DIAL libraries. Once I had done this small subsets of the entire NIST library worked. However the whole library (3Gb) doesn't provide any annotations in MS-DIAL or MS-FINDER. Is there a limit to the size of a .msp file these programs can use? Is there some way that I can test to see if MS-DIAL or MS-FINDER are loading the library correctly?

Thanks in advance.
Chris