Questions tagged [proteomics]

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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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35 views

Transcriptomics vs Proteomics for understanding molecular responses

I am planning some experiments to investigate how mono cultures of microbes respond to different nutrient concentrations. I want to use an -omics based approach to understand how, on a molecular level,...
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1answer
43 views

A database for RefSeq protein accession IDs

Are there any databases or tools that contain a list of all RefSeq protein IDs for the interest organism/microorganism, e.g. get a specific microorganism name and return all RefSeq Protein IDs that ...
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1answer
27 views

Help with DIA-Mass Spectrometry data analysis with several conditions (limma?)

I am trying to learn how to analyse normalised DIA-MS data and I am struggling with it :// The original dataset I got is (6 conditions (2 samples each)) with 3 technical replicates (total: 36 sample ...
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2answers
73 views

Block wise protein imputation

I am currently working on a dataset that contains 50 samples (10 samples * 5 blocks). The features of the date set are: The data is perfectly balanced between blocks, with equal treatment ...
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1answer
27 views

Holistic enzyme activity determination with computation [closed]

I'm currently working on a program which will determine the activity difference between an original enzyme and a variant with just 1 or 2 variants. Of course, I'm not talking about the "kinetic ...
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17 views

phosphosite nomenclature and conversion (phosphoproteomics)

I have a dataset containing the following kind of phosphorylation sites nomenclature: ...
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1answer
29 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
165 views

What unit is the length of a protein measured in?

Sorry if this question is obvious - I'm not familiar with proteomics so I'm not sure of the standard units. In this paper, it talks about using the length of a protein to calculate the NSAF value. ...
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How to calculate protein abundance from an .mzTab file?

I have an .mzTab file, with PRT and PSM values. Does anyone know of any specific functions that I could use to calculate protein abundance values from this data? More details This is a summary of ...
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1answer
26 views

Mapping protein refseq to Gene ID

I have a protein refseq (eg, NP_000029). How can I get the corresponding gene ID (ag, APC) from NCBI using an R package?
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1answer
110 views

median normalization for proteomics

I am using the data from a proteomics study were the data was log2 transformed and then a median normalization was applied. The data was normalized by groups of conditions (normal, mutant), not for ...
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1answer
64 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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63 views

How identifiable are human omics data and how to mitigate their identifying features?

Say a database were to store human omics datasets. The human subjects are known and the sample size is rather small in size initially (n=500). The database contains genomics, transcriptomics, ...
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20 views

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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693 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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2answers
106 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
26 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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110 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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1answer
405 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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1answer
62 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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1answer
68 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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1answer
105 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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30 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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0answers
16 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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96 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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2answers
1k 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
312 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) ...