LCMS based metabolomics by XCMS-METLIN?

More Swarnali Kar's questions See All

Is it possible to do Reitveld Refinement on single crystal XRD data?

I tried to do single-crystal Rietveld Refinement on my single-crystal XRD data using the option "refinement on single-crystal data/ integrated intensity data" in Fullprof but it is giving error...

30 January 2021 7,813 3 View

What will be the impact on Antenna performance to shift the resonant frequency by RLC Matching network?

There is always a possibility to shift the resonance frequency by adding a RLC matching network. I wonder what will be the consequence on antenna performance (axial ratio, gain)? If there is no...

13 September 2020 5,187 3 View

Axial ratio shows different result at different ortogonal setup. What could be the reason ?

17 June 2020 5,332 3 View

Firm survival and mortality: How to relate both?

I have two data sets 1. Age of all the surviving firms at any given point of time. The age distribution is an exponential function 2. The age of all the firms which died at a given point of time (...

01 February 2020 3,542 1 View

Why Antenna shows negative gain even though it has very good matching?

I am aware of the fact that electrically small antennas are poor radiators with very small gain and low efficiency. One main cause of this is poor matching. An extremly electrically small antenna...

19 January 2020 5,285 9 View

What is the impact of image current from ground plane on patch antenna? I wonder how it radiates if ground plane is very near to radiator?

As we know, patch antenna is combination of two magnetic dipole. If we place a perfect electrical conductor near a dipole, antenna performance will suffer significantly. Then how a patch antenna...

27 November 2019 7,597 5 View

I am getting two peaks at 702 and 705 eV for Fe 2p scan of a composite made from Fe-salen.how it can be explained?

the pure Fe-salen spectra is in conformity with literature,but the composite is showing two extra peaks at 702 and 705 eV. Can anybody explain about why the peaks are coming.

23 July 2019 5,710 3 View

What will be the cororidinate(theta and phi) to evaluate the axial ratio?

I have designed a circular polarized antenna. But , I am confused with cor-ordinate system. In some angel it shows less than 2 dB axial ratio and some other point it shows more than 10 dB like a...

23 May 2019 2,175 7 View

Why there is a big difference in between realize gain and gain in my design?

I have designed a multiport antenna. Where as, I have 2 dB Gain but realize gain is -6 dB. Point to be noted, S11 is really good. I have -25 dB return loss at my desired frequency.

22 November 2018 6,165 17 View

Bands in western blot are behaving like GHOST!!!!!!!!!!!!!!!!!?

I am doing western blot and after development I can see that one/ two lanes have no band. Perhaps, next day I am doing same gel run with same sample with no change in protocol, this time another...

25 September 2018 8,325 3 View

Can we classify HV and LV lines based on line length?

I have dataset which shows the length of power lines. I need to classify the lines based on the line length. Is there a rule to classify the High voltage (HV) and low voltage (LV) lines based on...

03 March 2021 4,116 4 View

No title

02 March 2021 3,060 3 View

Does Napabucasin soluble in dichloromethane and in ethanol?

I need to prepare a solution of Napabucasin (inhibitor of cancer cell stemness) in dichloromethane. The drug is expensive, so maybe somebody already tried to do it. If it is soluble, what is the...

02 March 2021 9,945 3 View

Issues with Permeabilization during Flow Cytometry?

Hello Everyone. Currently I am working to characterize macrophages in the myocardium after ischemia-reperfusion injury in rats. Due to the low total cell number isolated from rat hearts I can...

01 March 2021 3,867 3 View

Could you please recommend some good journal that accept very long revie papers (approximately 6000+ words) in neurosurgery, cancer biology ?

01 March 2021 8,087 3 View

Which cell line should we use to perform biological dosimetry experiments?

We are preparing some experiments based on irradiating cells under different conditions in order to evaluate the effects in terms of DNA damage, genetic expression, etc. As our project is...

01 March 2021 3,355 3 View

Is it possible for two human neuronal cell lines to have different gene sequence for the same protein?

I am looking at the ATP1A2 (Sodium/Potassium ATPase alpha subunit 2) in two human neuronal cell lines. Expression levels of this protein seems to be almost equal when detected by one antibody....

01 March 2021 3,607 3 View

Is CD44 degraded in lysosome together with hyaluronan after CD44 mediated endocytosis of hyaluronic acid?

Also when RHAMM binds hyaluronic acid, they get internalized, will RHAMM also be degraded? Or both CD44 and RHAMM will be transferred back to the cell membrane? Asking for breast cancer cell line...

01 March 2021 8,169 2 View

Do you need the CMV enhancer before the CMV promotor for a proper function of CMV on the gene that follows?

I'm a student and I have to produce a cell line with a knockin for the NRF2 gene with GFP. I have to put a promotor in front of the GFP because the gene will be too far away from the promotor of...

28 February 2021 7,127 2 View

What could be some reasons why unstimulated monocytes are getting activated?

Im doing PBMC isolation -> CD14+ enrichment using magnetic beads -> stimulation setup. My negative control is just cells in cRPMI but they seem to get activated over and over again.

28 February 2021 7,883 3 View

Harrie A Verhoeven

Daer Swarnali Kar, have you tried to convert your data from the Waters software into NETCDF format ? I have been testing XCMS a long time ago with Waters data, and I got them into XCMS using this format. I hope this helps, kind regards, Harrie Verhoeven.

Luca Narduzzi

1) yes it is fine. you can also convert the data to cdf using the WATERS' "Databridge" software. it is just a matter of choice.

2) the raw data format is a proprietary format of WATERS and can be analyze only by using WATERS' software. To use it with xcms, you need to convert it.

3) to use xcms, just follow this tutorial. It is from the guy that developed the last version of it.

https://bioconductor.org/packages/devel/bioc/vignettes/xcms/inst/doc/xcms.html

4) long way to go for the metabolites... follow the xcms guidelines and then METLIN will help you in the identification of the compounds.

Good luck!!!

Swarnali Kar

Thank you very much Luca Narduzzi for your comments. My question is does this Databridge software comes within waters Masslynx software or act as add in?

Also, thank you Harrie A Verhoeven for your answer. i wanted to convert it to NETCDF format. How can we do this conversion? We just have MassLynx software, Is it enough?

I started using XCMS, but now I am failing to upload data correctly. I have read the tutorial, but the data is no being saved. Can you suggest the step by step method to upload data in XCMS?

to find DataBridge:

Click Start > All programs > MassLynx > DataBridge

select the proper formats and that's all.

ok.

Thanks a lot Luca Narduzzi . I will definitely try it out.

Biswapriya Biswavas Misra

Hi,

This is a very interesting and relevant question for the entire research community working in metabolomics.

Please feel free to register (for free to create a login with your Email ID!) and join the International Metabolomics Society’s Forum: http://www.metabolomics-forum.com/index.php?action=forum;?action=forum#c12 to ask more specific questions any software, database, approach and platform (mass spectrometry, NMR) issues where you can get very specific responses from expert users and researchers!

Thanks again,

Biswa