Questions tagged [proteomics]

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How do protein-protein interaction databases work?

I am a student and just trying to gain a base level understanding of PPI databases and how to interpret their data. For example, when inputing multiple genes into String, does it only give protein-...
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31 views

Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) : cannot coerce class ‘“SeqFastaAA”’ to a data.frame

The example that I am trying to follow is this PGA tutorial. I want to use the information in the analysis of the mzML raw files from the proteomics data analysis. When I try to load the fasta file, I ...
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1answer
25 views

After completing the evaluation, how to predict PTM lysine or any other modification with unlabeled data for making a web server?

I have created a model with SVM classifier and evaluated it with 5-fold cross-validation. The dataset was sequence data containing lysine modified sites. Now I want to build a web server where anyone ...
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1answer
53 views

Running MaxQuant on Linux

I'm trying to run MaxQuant on a linux laptop, hower I'm constantly running into problems with MaxQuant crashing at different stages I tried to use mono 6.8 mono 5.4.1 on centos ubuntu each with ...
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56 views

Mapping a disease integrome on the whole genome

I'm currently studying a disease which has complex traits (non mendelian disease). Very few data are available on humans. But data collected from cell/animal models have been used to identify human ...
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2answers
54 views

How to download multiple proteomes at once?

I'm looking for a way to download multiple proteomes at once from one clade, as fasta. Probably from the NCBI, because it looks more user-friendly than Ensembl, but Ensembl is okay too. In the best ...
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1answer
19 views

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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27 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
69 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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10 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
56 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
16 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
71 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
151 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
11 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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1answer
65 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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68 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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54 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
628 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
223 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) ...