I am currently in the process of doing some data analysis for some MS/MS work I have been doing. I am planning to use SIRIUS (https://bio.informatik.uni-jena.de/software/sirius/) for molecular formula elucidation and structure prediction. SIRIUS needs centroided data, however, and unfortunately my MS2 analysis was all accrued out in profile mode. Additionally, the version of Xcalibur I used was several versions out of date (SP 2.2, rather than 2.9), so there . I understand that converting from .RAW to mzXML also converts the spectrum to centroid, but I have yet to find a software that then allows me to open .mzXML files and interact with the spectra, including exporting specific scans as .csv or .txt files. I need the raw data as text so that I can write my own .mgf files which contain the relevant information per energy level. I have tried software such as OpenMS and ProteoWizard, both of which seem to allow me to view spectra, but not exports the scans I am interested in. Could anyone suggest a free software that would allow me to do this?
Thanks a lot!
For quite a while I've been searching for a facility (preferentially Europe based) that would be capable of measuring relative changes in acetyl-CoA levels in extracts from cell lines cultured in vitro. Apparently it's not a routinely done quantification, I've already talked to some people about it and nobody had a good method to do it.
Any suggestions regarding the possible options would be highly appreciated.
I met the same problem as you. Have you already solved?
I used xcms2 on my lcmsms and have successfully executed the following commands.
#Load all libraries
I know that the searchmetlin is no longer available in xcms2. May i know how to extract the fragments with the parent ions out so i can do compound annotations ? I have tried the code as below but couldn't get it out.
xfragdata <- groupval(xfrag, value = "into")
I was checking my data quality before running PCA/PLS, but am confused by different articles I've read concerning this. Basically they say that Hotelling's T2 identifies severe outliers, and DModX identifies moderate outliers.
What I am seeing in my data:
-My QC's all cluster to the center of a PCA
- I have some samples located outside the Hotelling's T2 ellipse.
- Depending on how many PCA components I include in the DModX plot, I get different samples that are larger than the D-Crit value.
- How should I decide on how many PCA components to include in the DModX?
- Should I remove all outliers detected by the DModX graph and the Hotelling's T2 plot from my data set to prevent skewing of my PCA/PLS?
- Is it possible that the outliers could be of interest and I should leave them in further analysis?
I really appreciate any and all advice!!!!
Thanks Jan, couldn't have done it without your help!
Btw, i did saw the new XCMS interface. Since i'm still new in this i will play around with the old scripts and functions for sometime before trying out the new one.
I have a problem for viewing results. When I clicked the button "Results Table", nothing showed up. It seems that only multi-group results have this issue.
Does anyone have experience in solving this issue? Any response will be greatly appreciated.
Yes that should be a safe assumption.
I'm attaching the traceback and some of the data in xset below. There are files, but after i try the few
First i ran the scripts as below
> xset2 <- retcor(
Then i inspect the data in xset.
> str(xset, max.level = 2)
I still couldn't find out where is the bug you mentioned.
However, If i dont run the specify center=NULL, is it safe to say its running in NULL ?