how can outliers be removed from data before making a graph?

How do we ensure low abundant proteins seen in a proteome with as low as 1 PSM (peptide spectral match) are real and are indeed a part of the sample, not contaminants?

Also, please suggest what steps can be taken at each stage of mass spectrometry based proteomics for efficient QA and QC of the methods and results?

How the new bacterial secondary metabolites can be identified?

how can mass spectrometers be used to identify unknown compounds via molecular weight determination, or quantify known compounds, or determine structure and chemical properties of molecules.

I am working on LC-MS data having 3 biological replicates each for control and treated. how can we find out the relative abundance of proteins using unique peptide data?

Could you please describe the different variables in each step that could contribute to the difference in the final peptide analysis? And also how are the algorithms work to identify the different peptide isoforms?

Best methods to search for glycans?

The "FDR problem" for reporting the protein and peptides identifications in peptidomics and proteomics assays.

Curious how someone can learn LCMS based targeted proteomics?

Is there teaching any hands-on practices or software manual?

How to further analyze results of MS and go for target protein purification

Is it correct to normalize the data (for example by sample weight) before performing the batch correction? Or does the batch correction already include some kind of normalization?

Will you provide details for the data format of LC-MS data?

Hi, as a cell wall biologist, I am interested in the different carbohydrates that make up the wall matrix as well as their modifications during wall maturation. What are standard practices to analyze the combination of different carbohydrates in the wall?

I work with an enzyme that creates disulfide bonds with its substrates. I have developed a protocol to trap my enzyme to its substrate during the process of thiol oxidation using a thiol alkylating agent, N-ethyl-maleimide. This process covalently links the two proteins together via an inter-protein disulfide bond. I am now analyzing my data to identify the disulfide bonds generated and which cysteines are involved in any inter-protein disulfide bonds via mass spectrometry.

I want my results to have statical significance; what would be an appropriate number of replicate reactions to complete and run on MS? I would also appreciate any tips on ensuring that my results are reproducible between reactions.

How to determine if the marker of interest is protein's PTM in normal vs diseased state. If the hypothesis is PTM, how to pursue it further?

What are the probable major goals from this webinar? What all we will get to learn?

What would happen if I run only the actual samples replicates one by one and do not introduce QC samples in between? If I do not run the QC samples at all, how much reliable my data would be?

Is there any tips or tricks to minimise the interference during the analysis using LC-MS?

how to extract metabolites from soil samples 

While there are ways to analyze N-glycans, how do I characterize O-linked Glycans.

what are the effective methods and considerations for samples preparation for tissue phosphoproteomics

I have purified proteins. The purified protein was incubated with the extracted extracellular fluid from fungi. Specific protein bound interactors were run on gel. Comparing the bands with proper control I want to identify the interactor via LS-MS or MALDI. But the problem is that I am not getting in the gel. How can I troubleshoot the problem?

Several compounds drives during detection mass spectrometry for plasma analysis the library suggested different components which one best or correct

I want to study the metabolite profiling in plants under stressed and treated conditions. can you please suggests some methods and protocols regarding this?

What are the common mistakes one can make with Biological Mass Spectrometry?

Microalgae metabolomics analysis and draw a metabolite regulation diagram based on analysis

We get the Chromatogram, M/Z data, Fragmentation spectra when we perform the LCMS/MS analysis. The software embedded in the machine matches the obtained data with the MS library and provides us the best match which we consider it as the compound present in the sample. But, how confidently we can say that the identified compounds from the library is the actual compound and not the other compounds?

i am working on pegylation

My research depends mainly on compare a control with one or more treatments. The compare analysis is a demand. Currently, I have a GC/Ms data and I have to learn how could I deal with.

I am working in drug discovery field, mainly, invitro. By investigating new anticancer agents (Extracts, compounds...) I am always need to compare the change in metabolites with the counterpart controls. Is it enough to do that with only GC/Ms?

Many thanks for allowing me introduce my questions.

Critical factors for building a mass spec resource from scratch

Practical application for easily identification of novel drugs

No database for LC/MS

How should I do neurotransmitter (eg Acetylcholine, GABA, Dopamine) content analysis in C. elegans worms by LC-MS/MS and which column should be used in this case?

In statistics, rejection of outliers lead to increased precision of the method. With many replicates, the confidence intervals approaches zero and, as such, they cannot be used to estimate uncertainties of measurement. Therefore, disagreement between laboratories are ehanced when scientists report confidence intervals as if they were uncertainties, which, in fact, they are not. Eurachem and other organisations recommend to not reject outliers based on statistical evaluations, wimply in recognition of the impact it has on accuracy. It is a major conondrum in science, how it is possible for so many scientists to arrive at the expected conclusions of their investigations when outliers were rejected and the uncertainty is virtually zero. So, why do you start recommend the rejection of outliers when it contradicts scientific methodology?

I am planning for the mass spec based analysis of my IP pulldown of membrane proteins, it would be grerat to get the detailed description of the detergents compatible with the mass spectrometry.

LC MS functioning

I want to how how to analyse GCMS results and how to design the pathways based on our results using the software like gWAS

What's the minimal number of peptide spectral match to confirm the protein identification?

How to identify and quantify biomarkers in Clinical samples?

Protocol needed

Mass spectrometry to develop better means of enhancing the Immune system of the Birds. As can it help identifying the pathogen we are up against or not.

I am trying to develop a sample preparation pipeline that should ensure minimal downstream losses of low-abundance molecules.

Thanks in advance!

I am doing amino acid profiling mostly in new borns

i-Motifs are formed in the acidic pH (pH 3-4). How to maintain the same condition and which buffer and matrix should be used.

What is the efficient manner for fractionating and understanding ECM proteins by proteomics?

Please describe the working of Mass spectrometry and how can we use it to measure quantity of Nutrients in a Feed Sample.

I IP one protein from rice protoplast and want to know if there is a glycosylation site

at specific site.

However, the protein is too less, can only detected by silver staining, could't be detected by coomassie blue staining. Couldn't do glycopeptide enrichment neither.

In this event, how can i do to detect if there is a glycosylation site by LC/MS-MS ?

would like to learn how different mass spectrometry can be used in plant or animal genomics and proteomics?

mass spectronomy purpose and why use it in a research center

how to do data analysis and interpretation in Mass Spectrometry analysis?

I am interested specifically in:

1. Target protein acetylation site detection.

2. Target protein interrection with others (proteins interection).

3. Detection of proteins aggregation.

If you will give some related to this questions research examples, I would appreciate it alot.

Sample processing

How to prepare the pure samples from the total cell lysate?

How will LC-MS and GC-MS help in analysing secondary metabolite interaction of plants and microbes?

MS spectroscopy will help in Pharmacological studies

Plant metabolite extraction to understand plant immunity system

Spectroscopy is very interested

I extracted both phytohormones and sugars in the same sample using 70% methanol. What is the best LC column and solvents that can be used to separate these compounds in the same LC run? What are the best MS conditions?

It will be great if we could know how to adapt protocol for each case we can have. Thank you

How to Improve peak number while analyzing microbial samples using FI-MS?

interested in metabolomics study in diseases

I want to do a proteome analysis of a single chromosome. This includes proteins that are already identified and probably new, previously uncharacterized also. So which mass spec will be most suitable for getting good quality results?

The label-free quantitation (LFQ) method for assessing relative changes in the protein abundance in proteomics data.

I am working on Coronary artery disease in the underlying mechanisms. It would be great if the Webinar included a talk about Mass Spec can allow cataloging protein expression, and defining protein interactions is biological samples such as Blood (in diseases) .

How specialized quality control samples of varying sample complexity can be incorporated into experimental workflow?

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Plant samples from maize treated at varying osmotic stressors?