Skip to main content ↑ ↓
Topic: XCMS diffreport (Read 6067 times) previous topic - next topic

XCMS diffreport

Hi, I searched my LC-MS data obtained from Agilent HPLC-ESI-TOF MS against XCMS both online and offline. I have a few questions regarding the diffreport.

1. In the report (from both online and offline versions), there are two columns to the right of the "npeaks" column. These two columns are for the two groups of samples designated. I assume the numbers refers to the number of peaks detected in each sample group for a specific feature. However, I'm confused with the numbers. For example, my control group has 4 samples-080612-1, 080612-2, 080612-3, and 080612-4. In the column for "control" it says 0, but in the four columns for the 080612 samples the numbers are not zero. Sometimes in all four columns, the numbers are non-zero.

2. Regarding the column "maxint". Not sure where this number is from. Looking at my results, if the numbers under the captions "080612-1", "080612-2", "080612-3", etc referes to intensity as well then none of these numbers matches the "maxint".

3. The identity of the detected feature from online XCMS. The offline version provides metlin links for the identity of detected features, but the online version does not. I wonder if I want to know the potential identity of the detected feature from the online XCMS, how should I do it? The IDs from the offline is matched between mzmin and mzmax. Should I do the same thing with the online version, that is search against the range mzmin-mzmax?

Thank you very much for your time and kind assistance!

Re: XCMS diffreport

Reply #1 –
1.
Quote
but in the four columns for the 080612 samples the numbers are not zero
not sure what you mean here, can you post an example ?

2. maxint is the maximum absolute (not integrated!) intensity across all samples. You could say it is the intensity of the highest peak in the spectrum for this feature - from all your aligned samples.
  very useful if you need to decide if you can acquire MS/MS data for this feature

3. For XCMS Online, you can browse the METLIN hits directly online (click browse result table).
 In addition, the results.tsv table also included the METLIN hits with ppm and adduct information.

Re: XCMS diffreport

Reply #2 –
Hi Raf:
Thank you very much for your prompt reply. It’s much appreciated. Here I added more information, hoping you can understand my questions.
I checked the results from online version XCMS. There are total 3 tsv files, that is “result.tsv”, “XCMS.annotated.diffreport..control.vs.2_infected.tsv”, and “XCMS. diffreport..control.vs.2_infected.tsv”. These three files present the results in different ways, but “XCMS.annotated.diffreport..control.vs.2_infected.tsv” contains all of the information from “XCMS. diffreport..control.vs.2_infected.tsv”. Below are examples of my results from “result.tsv” and “XCMS.annotated.diffreport..control.vs.2_infected.tsv”.

I.   From online file “result.tsv”
featureidx   fold   tstat   pvalue   qvalue   fscore   mzmed   mzmin   mzmax   rtmed   rtmin   rtmax   maxint   dataset1_mean   dataset1_sd   dataset2_mean   dataset2_sd   isotopes   adducts   peakgroup   METLIN   name   METLIN_MSMS
1   9.270608412   9.295698488   1.97E-05   0.073481874   525   1014.810752   1014.809936   1014.814369   6.215   6.174   6.233333333   2287.241455   1293.330113   1594.283365   11989.95702   2032.769734   [899][M]+   [M+Na+NH4-H]+ 974.795 [M+Na+NH3]+ 974.795   74      M1015T6_2   n
2   11.15180468   8.541685442   7.38E-05   0.078827323   11   481.4599925   481.45823   481.4604859   6.878   6.771333333   6.923   3799.156738   1710.796207   1658.773222   19078.46515   4547.324526   [61][M]+      17      M481T7   n
3   6.782856554   7.153356857   0.000129677   0.078827323   765.5   731.6500957   731.6471024   731.6509431   6.371333333   6.270666667   6.399   1856.355957   1282.500757   1458.992213   8699.018665   1804.603714   [374][M]+   [M+H-C6H8O6]+ 906.668   36   6::DG(22:0/22:3(10Z,13Z,16Z)/0:0)[iso2]::M+H:: 4615|6::DG(22:1(13Z)/22:2(13Z,16Z)/0:0)[iso2]::M+H:: 4657|6::DG(20:2(11Z,14Z)/24:1(15Z)/0:0)::M+H::58947|6::DG(20:3(5Z,8Z,11Z)/24:0/0:0)::M+H::58975|6::DG(20:3(8Z,11Z,14Z)/24:0/0:0)::M+H::58995|6::DG(22:2(13Z,16Z)/22:1(13Z)/0:0)::M+H::59137|6::DG(24:0/20:3(5Z,8Z,11Z)/0:0)::M+H::59266|6::DG(24:0/20:3(8Z,11Z,14Z)/0:0)::M+H::59267|6::DG(24:1(15Z)/20:2(11Z,14Z)/0:0)::M+H::59294   M732T6   n

II.   From online file “XCMS.annotated.diffreport..control.vs.2_infected.tsv”
   name   fold   tstat   pvalue   qvalue   fscore   mzmed   mzmin   mzmax   rtmed   rtmin   rtmax   npeaks   control   2_infected   maxint   mean1   sd1   mean2   sd2   080612orgnic_12_pos.mzdata   080612orgnic_13_pos.mzdata   080612orgnic_14_pos.mzdata   080612orgnic_15_pos.mzdata   080612orgnic_10_pos.mzdata   080612orgnic_4_pos2.mzdata   080612orgnic_5_pos.mzdata   080612orgnic_6_pos-r001.mzdata   080612orgnic_7_pos.mzdata   080612orgnic_8_pos.mzdata   isotopes   adduct   pcgroup
1   M1015T6_2   9.270608412   9.295698488   1.97E-05   0.073481874   525   1014.810752   1014.809936   1014.814369   6.215   6.174   6.233333333   4   0   4   2287.241455   1293.330113   1594.283365   11989.95702   2032.769734   0   72.17832887   1744.347061   3356.795062   10037.54323   11057.83482   10374.32182   14139.78433   14895.14339   11435.11455   [899][M]+   [M+Na+NH4-H]+ 974.795 [M+Na+NH3]+ 974.795   74

1.   My number 1 question asked yesterday regarding the table in XCMS.annotated.diffreport..control.vs.2_infected.tsv. As shown in the table, there is a column “control”, which says “0”. However, when I looked at the individual control samples, which are 080612organic_12_pos.mzdata, 080612organic_13_pos.mzdata, 080612organic_14_pos.mzdata, and 080612organic_15_pos.mzdata, only one column says zero. I wonder if the columns “control” and for the individual control samples refer to the same thing, like peak intensity.
 Raf, you said that the result.tsv file contains Metlin hits. I don’t think I’m clear about this. As the table shown above, there are columns “adducts” and “Metlin”. In the example above, “adduct” says [M+Na+NH4-H]+ 974.795 [M+Na+NH3]+ 974.795; “Metlin” is blank. For another feature, “Metlin” says 6::DG(22:0/22:3(10Z,13Z,16Z)/0:0)[iso2]::M+H:: 4615|6::DG(22:1(13Z)/22:2(13Z,16Z)/0:0)[iso2]::M+H:: 4657|6::DG(20:2(11Z,14Z)/24:1(15Z)/0:0)::M+H::58947|6::DG(20:3(5Z,8Z,11Z)/24:0/0:0)::M+H::58975|6::DG(20:3(8Z,11Z,14Z)/24:0/0:0)::M+H::58995|6::DG(22:2(13Z,16Z)/22:1(13Z)/0:0)::M+H::59137|6::DG(24:0/20:3(5Z,8Z,11Z)/0:0)::M+H::59266|6::DG(24:0/20:3(8Z,11Z,14Z)/0:0)::M+H::59267|6::DG(24:1(15Z)/20:2(11Z,14Z)/0:0)::M+H::59294. First of all, as in the example, what “+974.795” means and why there are [M+Na+NH4-H] and [M+Na+NH3]? Second, if “Metlin” column is blank does it mean the feature is not identified by Metlin? Third, how  to read 6::DG(22:0/22:3(10Z,13Z,16Z)/0:0)[iso2]::M+H:: 4615|6::DG(22:1(13Z)/22:2(13Z,16Z)/0:0)[iso2]::M+H:: 4657|6::DG(20:2(11Z,14Z)/24:1(15Z)/0:0)::M+H::58947|6::DG(20:3(5Z,8Z,11Z)/24:0/0:0)::M+H::58975|6::DG(20:3(8Z,11Z,14Z)/24:0/0:0)::M+H::58995|6::DG(22:2(13Z,16Z)/22:1(13Z)/0:0)::M+H::59137|6::DG(24:0/20:3(5Z,8Z,11Z)/0:0)::M+H::59266|6::DG(24:0/20:3(8Z,11Z,14Z)/0:0)::M+H::59267|6::DG(24:1(15Z)/20:2(11Z,14Z)/0:0)::M+H::59294?
2.   In the file “result.tsv”, there are columns named “isotopes” and “peakgroup”, I wonder what the numbers in these columns mean?
3.   Raf, you said “maxint” is the maximum absolute (not integrated!) intensity across all samples. I wonder then what are the numbers in columns for individual samples, such as for “080612organic_12_pos.mzdata” shown above, refer to?

Again thank you very much for your time and kind assistance!

Re: XCMS diffreport

Reply #3 –
1. yes, not all features have METLIN hits. That is normal. There are many unknown metabolites ...
2. please search the forum for these keywords. This question has been asked several times already.
3. the values in the columns for the samples are the integrated intensities. maxInt is just additional information, for example to see if the intensity of this compound is high enough for MS/MS analysis,