How can I analyze Waters Q-TOF MSe Data?

More Bassel Sabbagh's questions See All

Can a journal be ISI, scopus, and pubmed indexed and still a predatory journal?

I've noticed that some publishers and journals have a very fast review process, with high acceptance rates for articles regardless of their novelty and quality, as long as you pay APCs. Some of...

15 June 2020 8,899 8 View

How do i create triggered pulse generator in simulink ?

hello all, In Simulink : how can I create a single pulse of: amplitude = 1, width = 300 sec (for example) when ever the input changes from 0 to 1 (otherwise it equals 0) ? thanks

03 August 2019 3,784 3 View

What is the best method for determination of soil total elements content including Si?

I want to determine total elements (both major and trace elements) in soil samples . Could you suggest me a digestion method which able to completely dissolve the soil sample. Thanks

12 February 2018 2,026 9 View

What is the reason of secondary bands in low annealing temperatures in gradient PCR?

26 December 2015 8,102 3 View

error in running a model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

error in modelling model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

MGL tools

20 June 2021 0 0 View

i have some problem with chtMultiRegionSimpleFoam

--> FOAM FATAL ERROR: Maximum number of iterations exceeded From function Foam::scalar Foam::species::thermo::T(Foam::scalar, Foam::scalar, Foam::scalar, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar) const) const [with Thermo = Foam::hConstThermo >; Type = Foam::sensibleEnthalpy; Foam::scalar = double; Foam::species::thermo = Foam::species::thermo >, Foam::sensibleEnthalpy>] in file /home/ubuntu/OpenFOAM/OpenFOAM-4.1/src/thermophysicalModels/specie/lnInclude/thermoI.H at line 66. FOAM aborting #0 Foam::error::printStack(Foam::Ostream&) at ??:? #1 Foam::error::abort() at ??:? #2 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::calculate() at ??:? #3 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::correct() at ??:? #4 ? at ??:? #5 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6" #6 ? at ??:?

24 March 2021 0 0 View

What is your perception on using visual analysis or quantitative approaches to evaluate data from single-case research designs (n of 1 trials)?

Results of single-case research designs (i.e., n-of-1 trials) are often evaluated by visually inspecting the time-series graph and computing quantitative indices. A question our research team is...

03 March 2021 687 1 View

After a reference from Int J Body Compos Res, can any body help?

Hi, I am after the reference below, my library says it cannot obtain a copy either locally or internationally, any help appreciated! Chris Wang ZM, Heshka S, Wielopolski L, Pi-Sunyer FX, Pierson...

03 March 2021 6,193 1 View

Resistor definition in Piezoelectric bimorph with ANSYS workbench

Hello, good day! I am trying to simulate similar bimorph piezoelectric harvester with below commands. However, the output power doesn't change with resistor value. Please help to find the reason. ET,10,CIRCU94,0 !SET UP RESISTOR R,1,100000 !RESISTANCE VALUE TYPE,10 !SET ELEMENT TYPE E,1,2 !CREATE RESISTOR BETWEEN NODES 1 AND 2 Thanks in advance Regards,

02 March 2021 0 0 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

Is there a powerful system for the security of the systems distributed on IoT systems?

02 March 2021 3,858 10 View

Peter G Hains

Have a look at ProteoWizard, it will convert your files for you. Depending on what you want to do Skyline may be able to help. Skyline is about quantitation, not identification. How well they work with MSe data, I can't say as I've never actually tried this.

http://proteowizard.sourceforge.net/

https://skyline.gs.washington.edu/labkey/project/home/software/Skyline/begin.view

Bassel Sabbagh

Hello Peter,

Skyline is not going to help me in this situation, i want first to identify peptides in the mixture. Proteowizard does not support MSe files

St John Skilton

Hi Bassel, Actually, that's why we have just released versions of Byonic and Byologic which process Waters MS^E data alongside data from Thermo, Bruker, Agilent and SCiex. Our customers wanted that capability. There's a link on our updates page which has an example of that data processing in Anna Schwendeman's lab in Michigan, which processed SYNAPT data ; https://www.linkedin.com/company/protein-metrics-inc-?trk=co-feed-recent-comments. There's a peer-reviewed paper out shortly, so I can't send that yet, sorry.

You can get FREE trial downloads here: http://www.proteinmetrics.com/contact-us/request-demo/

I used to work at Waters and was involved in the development of those packages you mention, feel free to ask me on [email protected].

Regards

St John

Hello St John, great! i would try the software. I think in my case Byonic would be helpful becasue i want to use it for identification

Pierre Pétriacq

Hi,

Have a look at Progenesis from Waters. The software is quite expensive but supports MSe data analysis. If you ask for a demo, you might be able to try it first and see if it helps. Personally, I treat MSe data in MassLynx only for confirmation purposes (ID validation of small metabolites). Good luck.

Hi Pierre, yes progenesis is auite expensive. i need to identify peptides so Masslynx alone is not enough

Robert Hardt

Hi Bassel,

You could try DIA-Umpire (http://diaumpire.sourceforge.net). Should be able to handle MSe data.

Robert

Osnat Hakimi

Anyone with experience using the DIA-Umpire? What are the recommended PC specifications?

We have been using Progenesis but recently having memory-related problems and it keeps getting stuck

will appreciate any thoughts on this...

Osnat

Jose Courty

Somebody knows if we can treated the MSe data from Waters machine with Masquant sofware ?

Best regards

José

Hi Jose,

Do you mean Mascot? As far as I know for .raw MSe files you must use the waters software (Progenesis or PLGS)

Thank you,

Yes Mascot or other freeware. Can we treated our .raw MSe files to used other free software (MasQuant or other) ?

I have the same problem... so far I could not find any software to process my files, only the waters one. It depends on your acquisition mode... DDA or DIA, with the latter only compatible with Waters software.

Hope this helps