Questions tagged [proteomics]

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How to map selected genes to Metabolic pathway Maps

I have a selected Arabidopsis Genome Initiative (AGI) list for RNA seq and proteomics data, how can I map them to metabolic pathway maps to vilualize(e.g. TCA cycle / FA / Photosynthesis) in KEGG or ...
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19 views

Principle of TMT Tags in Multiplex Proteomics

I am new to proteomics research and analyzing mass-spec data. I am trying to learn more about the theory/principle of TMT tagging (a type of isobaric labeling) coupled with LC-MS/MS spectrometry. I ...
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2answers
64 views

Proteomics data Vs Transcriptomics data?

I want to use either of Proteomics or Transcriptomics data for integrating it into my kinetic model. Before proceeding, I want to know what are the advantages of using either of them so that I could ...
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8 views

How to integrate the transcriptomics data with kinetic metabolic models?

I have created a convenience kinetics model. Now, I want to integrate the transcriptomic data with my convenience kinetics* model for altering/weighing the kinetic parameter values. I read some ...
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1answer
54 views

How I normalize these two sets of data

I have average log fold change for a cluster of cells versus another cluster of cells by Seurat like below ...
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0answers
13 views

What is the purpose of the “fixedSearchFolder” and “fixedCombinedFolder” in MaxQuant?

What is the purpose of changing the fixedSearchFolder and fixedCombinedFolder in MaxQuant proteomics software? Is there any data ...
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1answer
55 views

Preparing PDB file for modeling with Swiss-Model

I recently starting studying bioinformatics and have a question. I need to build a model of protein using Swiss-Model. First, I need to download a protein record from PDB (for example, 2HZI), then I ...
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1answer
87 views

What is the purpose of 'Folder locations' in MaxQuant?

MaxQuant is a tool for proteomics quantification. In the settings under Global parameters / Folder locations are three folder locations that are possible to be ...
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0answers
8 views

Can MSstatsTMT be used for both MS2 and MS3 runs?

MSstatsTMT is an R library for statistical analysis of TMT labeled mass-spectrometry (MS) proteomics data. The documentation does not explicitly mention the kind of MS that can be processed. The ...
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17 views

A well defined, prokaryotic, TMT labeled dataset for testing and development?

I am looking for a dataset to test and develop our proteomics downstream analysis pipeline. What data could we use? We ideally need TMT 11-plexed samples (raw files collected with Thermo-Fisher's ...
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1answer
63 views

Why does a missing label 11plex TMT shows up at almost 50% intensity compared to other labels?

We have a test plate that was done with 10 of the 11plex TMT labels. So, the intensities of the 11th label should be almost zero, plus the leakage from the 10th label due to 13C content. Although we ...
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0answers
57 views

How to do protein quantification with Peptideshaker output (TMT labeled, MS2)?

I have TMT tagged MS2 mass spec run processed with Peptideshaker. I saved the project in a peptideshaker format cpsx. Now, I would like to do the quantification ...
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0answers
53 views

Block wise protein imputation

I am currently working on a dataset that contains 50 samples (10 samples * 5 blocks). The data is perfectly balanced between blocks, with equal treatment representation in each block. Each block ...
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2answers
391 views

Omics data: How to interpret heatmap and dendrogram output?

How to interpret heat map and dendrogram output for biological data (omics) in words (when writing results and discussion)? What should I consider (statistics behind?) and what is the best approach? ...
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1answer
173 views

How to interpret PCA output statistically and biologically?

How can I interpret the PCA results statistically for biological data? I have used FactoMineR and factoextra libraries for PCA Scripts used: library(FactoMineR) ...