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1
Hi all,

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 Additionally, the version of Xcalibur I used was several versions out of date (SP 2.2, rather than 2.9), so there .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!
2
Compound identification / Acetyl-CoA measurements
Last post by Anna_Nieborak -
Hi!
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.
3
XCMS Online / Re: Results Table cannot be displayed
Last post by leizhang -
Hi Dan,

I met the same problem as you. Have you already solved?

Best

Lei
4
XCMS / export XCMS2 fragments
Last post by gooooh -
Hi,

I used xcms2 on my lcmsms and have successfully executed the following commands.

Code: [Select]
#Load all libraries
library(xcms)

#Create and spacify filepath
path <- "G:/msms"
files <- list.files(path, full.names=TRUE, pattern="cp.mzXML", recursive = TRUE)


xrawctrl <- xcmsRaw(files[1], includeMSn = TRUE)
peaks <- findPeaks(xrawctrl, method="MS1")
xs <- xcmsSet(files, method="MS1")
xfrag <- xcmsFragments(xs)

Code: [Select]
> xfrag
An "xcmsFragments" object with  5819  peaks in 912 Spectra
From Level 1 to 2 Number of Samples:  1 .

Sample 1 :
    646 Peaks in Level 1
    5173 Peaks in Level 2

Memory usage: 0.402 MB

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.

Code: [Select]
xfragdata <- groupval(xfrag, value = "into")
write.csv(xfrag, file="xfrag.csv")


Thank you.

Regards.
5
Other / Dealing with outliers...
Last post by rebeccaweed -
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.

My questions:
           - 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!!!!
6
XCMS / Re: Error when executing xcmsset
Last post by gooooh -
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.
7
METLIN / Re: can not visit Metlin
Last post by Cindyhello -
I think in China you need a VPN
8
XCMS Online / Results Table cannot be displayed
Last post by Dan -
Hi there,

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.

Thanks,
Dan
9
XCMS / Re: Error when executing xcmsset
Last post by Jan Stanstrup -
Yes that should be a safe assumption.
10
XCMS / Re: Error when executing xcmsset
Last post by gooooh -
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
Code: [Select]
> xset2 <- retcor(
+   xset,
+   method = "obiwarp",
+   profStep = 1,
+   plottype = "deviation",
+   center = NULL,
+   col = NULL,
+   ty = NULL,
+   response = 1,
+   distFun = "cor_opt",
+   gapInit = NULL,
+   factorDiag = 2,
+   factorGap = 1,
+   localAlignment = 0,
+   initPenalty = 0)
center sample:  
Processing: Error in if (!file.exists(object)) stop("xcmsSource: file not found: ",  :
  argument is of length zero

> traceback()
11: .local(object, ...)
10: xcmsSource(filename)
9: xcmsSource(filename)
8: xcmsRaw(object@filepaths[center], profmethod = "bin", profstep = 0)
7: .local(object, ...)
6: retcor.obiwarp(object, ...)
5: retcor.obiwarp(object, ...)
4: do.call(method, alist(object, ...))
3: .local(object, ...)
2: retcor(xset, method = "obiwarp", profStep = 1, plottype = "deviation",
       center = NULL, col = NULL, ty = NULL, response = 1, distFun = "cor_opt",
       gapInit = NULL, factorDiag = 2, factorGap = 1, localAlignment = 0,
       initPenalty = 0)
1: retcor(xset, method = "obiwarp", profStep = 1, plottype = "deviation",
       center = NULL, col = NULL, ty = NULL, response = 1, distFun = "cor_opt",
       gapInit = NULL, factorDiag = 2, factorGap = 1, localAlignment = 0,
       initPenalty = 0)

Then i inspect the data in xset.

Code: [Select]
> str(xset, max.level = 2)
Formal class 'xcmsSet' [package "xcms"] with 15 slots
  ..@ peaks           : num [1:6117, 1:11] 379 421 397 471 235 ...
  .. ..- attr(*, "dimnames")=List of 2
  ..@ groups          : num [1:116, 1:9] 181 236 249 255 279 ...
  .. ..- attr(*, "dimnames")=List of 2
  ..@ groupidx        :List of 116
  ..@ filled          : int(0)
  ..@ phenoData       :'data.frame': 46 obs. of  1 variable:
  ..@ rt              :List of 2
  ..@ filepaths       : chr [1:46] "G:/tissue/mzxml/np/neg/CASE/D N 1.mzXML" "G:/tissue/mzxml/np/neg/CASE/D N 2.mzXML" "G:/tissue/mzxml/np/neg/CASE/D N 3.mzXML" "G:/tissue/mzxml/np/neg/CASE/DN 4.mzXML" ...
  ..@ profinfo        :List of 2
  ..@ dataCorrection  : int(0)
  ..@ polarity        : chr(0)
  ..@ progressInfo    :List of 15
  ..@ progressCallback:function (progress) 
  ..@ mslevel         : num(0)
  ..@ scanrange       : num(0)
  ..@ .processHistory :List of 46
> head(xset@peaks)
           mz    mzmin    mzmax      rt   rtmin   rtmax
[1,] 379.1944 379.1942 379.1948  97.324  79.794 112.823
[2,] 421.2051 421.2044 421.2053 108.454  87.215 119.562
[3,] 397.1605 397.1600 397.1609 112.486  92.272 124.966
[4,] 471.1973 471.1968 471.1977 112.823  92.609 121.588
[5,] 235.1809 235.1807 235.1810 120.573 105.423 128.338
[6,] 463.2157 463.2154 463.2162 121.249 108.454 129.683
          into      intb  maxo   sn sample
[1,]  63585.88  63243.50 18469  281      1
[2,] 126455.21 125712.75 20504  184      1
[3,] 112149.18 112028.20 16132  697      1
[4,] 111377.42 111166.17 19105  354      1
[5,] 128713.22 128676.36 31172 1242      1
[6,]  62646.78  62619.22 10310  509      1
>

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 ?

Thanks.