Questions tagged [proteomics]

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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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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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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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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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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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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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101 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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phosphosite nomenclature and conversion (phosphoproteomics)

I have a dataset containing the following kind of phosphorylation sites nomenclature: ...
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696 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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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 ...