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1
MS-DIAL / MRMPROBS Crashing When Importing Converted Thermo LC-MS/MS mzML Files
Last post by TM -
I am encountering a problem with the MRMPROBS software when I try to import mzML files that have been converted from Thermo raw files (LC-MS/MS). The software crashes upon this operation.

Additionally, when I press the "Finish" button in the reference options, the software abruptly terminates. I am struggling to understand the underlying cause of these issues.

I would appreciate your assistance in resolving this problem. Could you provide any insights or solutions for this issue?

I look forward to your response.

Thanks,
TM
2
MS-DIAL / Linux add export parameter for choose export raw data matrix of Area or Height
Last post by Ruth -
Hi，
   MS-DIAL is the most excellent software that I have used. MS-DIAL can not only support analyze in Linux but also process the MSE spectral data.  So I am very approciate your work. I am trying to use MS-DIAL to identification and annotation the metabolites.
   Recently, I found the Alignment msdial result (the raw matrix) is the matrix of Height, but I am in need of the matrix of Area instead of the matrix of Height, cause I feel Area data is more accurate than Height data. So could you please update your software of Linux platform which include the parameter to choose which type of raw data matrix to export, Height or Area.
   By the way, this is how I do in Windows version to get the Area data, I want to have the same Area data in Linux, too. Could you please help me about this requirement?

Best,
Ruth


3
MS-DIAL / Re: Question about Bruker QTOF raw data in MS-DIAL
Last post by hdecoevo -
I received an answer to the above question from the ABF converter developer, and am posting it in case it helps others. The converter currently can't process .tdf or .tdf_bin files because CompassXtract does not recognize them. There is a new converter in the works designed to do so, but a release date hasn't been announced. For now it seems it isn't possible to process IMS data in MS-DIAL, and files should be converted to a more general format (like mzXML) directly from Bruker software.
4
MS-DIAL / Batch alignment in MS-DIAL 4.92
Last post by Hzamora14 -
Hi all,

Does MS-DIAL handle batch alignment for GC-MS data?

I know you are asked to indicate the batch ID in the project settings, but I am not clear if that information are used for doing batch alignment during the process.

Thanks!
5
MS-DIAL / Re: Question about Bruker QTOF raw data in MS-DIAL
Last post by hdecoevo -
A quick revision to my previous post - I realized my error (trying to drag and drop the .tdf file, rather than the .d folder from Bruker). But unfortunately, the ABF converter is still telling me it can't convert the .d file folders to .abf because CompassXtract isn't installed. I've installed, uninstalled, and reinstalled it multiple times now. Has anyone else had this issue?
6
MS-DIAL / Re: Question about Bruker QTOF raw data in MS-DIAL
Last post by hdecoevo -
Hello! I have a related follow-up question and would really appreciate any guidance. I similarly have TIMS-TOF-PASEF data, with data-independent acquisition on a Bruker system.

I have tried to use the ABF converter after downloading both Compass Xtract and the TDF-SDK library from Bruker. Is there something that needs to be done to those intermediaries after they are downloaded, or does the ABF converter just 'know' to search the program files for the dll and library files they contain? Because even after those downloads, the ABF converter is still telling me that the .d files are not an accepted format.
7
MS-DIAL / MS-DIAL Hard ionization (GC/MS) greyed out
Last post by eshe -
Hi,

I am trying to process GCMS files (converted to ABF) but when I am setting measurement parameters it will not allow me to select Hard ionization (GC/MS). The button is greyed out.

I have tried versions 5.0.6, 5.1.230429 and 5.1.230517. All 3 have the button greyed out. Is there a setting I am missing?

Thanks.
8
Job opportunities / Eight International Fellowships in Metabolismat CBMR, University of Copenhagen
Last post by signatur -
Eight International Fellowships in Metabolism
Novo Nordisk Foundation Center for Basic Metabolic Research
University of Copenhagen

The University of Copenhagen seeks 3 PhD students and 5 Postdoc fellows to commence on January 1, 2024, at the Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR).

The PhD student and Postdoc fellowships are part of the CBMR International PhD & Postdoc Program.

Job description
The fellowships are aimed at early-career researchers with a basic science background or clinicians who aspire to a career in academia. We are particularly interested in candidates who are familiar with integrative research approaches within the broad area of basic cardiometabolic research with an application towards human pathophysiology.
CBMR’s mission is to lead collaborative interdisciplinary research from single-cell genomics to whole-body systems, transforming the basic understanding of cardiometabolic health, and accelerating its translation into prevention and treatment strategies. For more information about CBMR, please visit our website.

Research projects open for applications
The eight research projects and their corresponding Principal Investigators are listed below. More information about each of the positions and how to apply can be found at CBMR International PhD & Postdoc Program – University of Copenhagen (ku.dk)

PhD projects
1. Principal Investigator Associate Professor Atul S. Deshmukh
“Identification and Characterization of In Vivo Secreted Adipokines in Health and Disease”

2. Principal Investigator Professor Kei Sakamoto
“Regulation of the Salt-Inducible Kinases in Control of Hepatic Gluconeogenesis”

3. Principal Investigator Associate Professor Karin Tybjerg
“Technology Platforms as Interdisciplinary and Epistemic Hubs”

Postdoc projects
1. Principal Investigator Professor Ken Arnold
“Practicing Participation: Stakeholder Engagement Processes across International Museums”

2. Principal Investigator Associate Professor Thomas Frimurer
“GPR39 Agonists for the Treatment of Obesity, Type 2 Diabetes and NAFLD”

3. Principal Investigator Associate Professor Marta Guasch-Ferré
“INTEROMICS: Integration of Dietary and Lifestyle Factors with -Omics Data for the Prevention of Cardiovascular Disease”

4. Principal Investigator Associate Professor Jordi Merino
“A Single-Cell Perspective to the “Common Soil” Hypothesis for Diabetes and Cardiovascular Disease”

5. Principal Investigator Professor Thomas Moritz
“In Vivo Labeling Combined with Tissue-Specific Metabolic Flux Analysis and Interconnected Metabolic Modeling”

Questions
Questions regarding the CBMR International PhD & Postdoc Program can be directed to cbmr@sund.ku.dk.

International applicants can find more information on the International Staff Mobility webpage.

Application
This advert is an extract and cannot be used as the basis for an application. The full text for each of the eight research projects, as well as a link to the application system, are available at CBMR International PhD & Postdoc Program.

The deadline for applications is June 18, 2023.

9
MS-DIAL / Error: you don't have any alignment result file
Last post by Yxf00678 -
Dear Metabolomics Community,

I urgently need to solve the Problem connected to the following error message. Does anyone know the reason for this error?

I need to trasport the MS/MS data into the mzML. file in order to have an analytical of FBMN in GNPS.
But when I choose the "Export"\“Alignment Result”, it pops up and say
"You don't have any alignment result file"

Please have a look to the screenshot.
 
How should I solve the problem? Any advice or suggestions would be much appreciated.

Cheers,
Yxf