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High resolution data and findMsMsHR.mass #104
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So, a few things here: |
Hi, you probably want to change your limit.fine and limit.coarse parameters - both are in mass units (not in ppm). So basically here you are building the EIC with a mass window from 175.8937 to 185.8937, and accepting MS/MS precursor ions in a range of 100 mass units (50 above and 50 below your mass). For the limit.coarse (the acceptance limit for the precursor in an MS2 scan), a reasonable number might be 0.3 or so (i.e. you accept MS2 with a precursor from 180.6 to 181.2) and for the limit.fine, depending on your instrument, some 5 or 10 ppm? (which you can calculate with As Emma said, we haven't used the mzXML format in ages. It might even work but it's untested and using mzML instead might work. Your deprofile argument looks mangled, what are you trying to do? Are your data profile mode and need to be centroided (in which case you can use e.g. deprofile = "deprofile.fwhm")? You might alternatively want to deprofile during conversion to mz(X)ML (in ProteoWizard: the "peak picking" option), since the RMassBank deprofiler is comparatively slow. If your data is already centroid mode, use deprofile = NA. What instrument are you using? If the error persists (and it might), would you give us the raw files and a complete script to check? |
Depending what instrument, could this error could be resolved with the fillPrecursorScan=TRUE in the settings.ini file? Define raw MS retrieval settings.findMsMsRawSettings: |
Thank you for the comments. source("http://bioconductor.org/biocLite.R") This gave me versions 1.8.1. I updated to v1.9.1 that is also available on the Bioconductor website (I couldn't install your tar.gz package since I am working on a W7 computer, however if there are significant differences I will attempt to install with Rtools). The files were acquired on a Q-Exactive MS. I re-converted the data to mzML, selecting levels 1- and peak picking to centroid the data prior to reading into r using the following: msms_1<- openMSfile("DW-141208-GG-01.mzML", verbose= FALSE) I then updated the function to the following (I switched fillPrecursorScan to both TRUE and FALSE with the same results): l1<- findMsMsHR.mass(msms_1, mz= 180.8937, limit.coarse= 0.3, limit.fine= ppm(180.8937, 10, p=TRUE), rtLimits= NA, maxCount= NA, Upon which I receive the following error: Which was the same as before. We are hoping to incorporate the RMassBank package into our MSMS confirmation workflow from untargeted metabolomics. The data was acquired using 2 different scan events, an MS1 scan from 50-500 and MS2 scan for 180.8937 +/- 0.5. I have no problem sharing the data file with you. Thanks again for all your help. |
The Q-Exactive shouldn't need the fillPrecursorScan option (at least not so far). but with the path and file name adjusted to the latest version number and the actual location of the tar.gz file on your machine? Thanks! From: dwalke04 [notifications@github.com] Thank you for the comments. source("http://bioconductor.org/biocLite.R") This gave me versions 1.8.1. I updated to v1.9.1 that is also available on the Bioconductor website (I couldn't install your tar.gz package since I am working on a W7 computer, however if there are significant differences I will attempt to install with Rtools). The files were acquired on a Q-Exactive MS. I re-converted the data to mzML, selecting levels 1- and peak picking to centroid the data prior to reading into r using the following: msms_1<- openMSfile("DW-141208-GG-01.mzML", verbose= FALSE) I then updated the function to the following (I switched fillPrecursorScan to both TRUE and FALSE with the same results): l1<- findMsMsHR.mass(msms_1, mz= 180.8937, limit.coarse= 0.3, limit.fine= ppm(180.8937, 10, p=TRUE), rtLimits= NA, maxCount= NA, Upon which I receive the following error: Which was the same as before. We are hoping to incorporate the RMassBank package into our MSMS confirmation workflow from untargeted metabolomics. The data was acquired using 2 different scan events, an MS1 scan from 50-500 and MS2 scan for 180.8937 +/- 0.5. I have no problem sharing the data file with you. Thanks again for all your help. — |
Hi again, just by looking at your code I don't see anything wrong, so it's probably something that I could best look at with the actual data file. If you upload it somewhere I'll happily look into it... |
This is on hold until we have a data file @dwalke04 it would be great if you could contact us directly! |
Any update? I am having a same issue |
As mentioned in the issue trace, without data or more information, we cannot debug or recommend what to do. This is the first report since the original message...
If you are having issues, please provide more information as to your exact problem, thanks.
…----------------------------------------------
PI: EnvCheminf @ LCSB
FNR ATTRACT Fellow
emma.schymanski@uni.lu
On Fri, Feb 15, 2019 at 8:23 PM +0100, "kg737" <notifications@github.com<mailto:notifications@github.com>> wrote:
Any update? I am having a same issue
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Attempting to extract data from mzXML file containing ms1 and ms2 scan (two total).
Read file in using mzR:
ms_file<- openMSfile("141208-GG-01.mzXML")
Completed successfully
Attempted to extract spectra for the given precursor mass:
l1<- findMsMsHR.mass(ms_file, mz= 180.8937, limit.coarse= 50, limit.fine=5, rtLimits= NA, maxCount= NA, headerCache= header(ms_file), fillPrecursorScan= TRUE, deprofile= getOption("RMassBank", noise = NA, method ="deprofile.fwhm", colnames = TRUE )$deprofile)
However, I keep receiving the following error message:
Error in
colnames<-
(*tmp*
, value = c("mz", "int")) :'names' attribute [2] must be the same length as the vector [0]
In addition: Warning message:
In is.na(headerCache) :
is.na() applied to non-(list or vector) of type 'NULL'
Thanks!
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