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Questions tagged [proteomics]

Large scale study of proteins.

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How to take precise/low number of cells from cell lysate? [closed]

I would like to know that how can we take low or precise number of cells from a cell lysate? (without using any protein quantification assay). Let say, If I have a cell line having cell density 5x10^...
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1answer
27 views

What are the advantages of iTRAQ/TMT technology over electrophoresis?

I'm currently working on the paper regarding proteomics research. I've listed a lot of questions that freshmen may have during their study. Can anyone explain (based on your experience in the lab) the ...
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1answer
76 views

Why is the macromolecular composition of a human cell seemingly hard to find?

I am trying to find a 3D rendering or list of molecules by volume in a cell (originally I was searching for human, but I'll take any at this point!). I understand the open-endedness of the question: ...
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2answers
164 views

What happened to ProteomeCommons.org?

ProteomeCommons.org seems to once have been a resource for raw proteomics data. Thought, the website now offers gardening tools. It seems to be hacked. Does anyone know whether the data is still ...
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0answers
11 views

transcriptional modulators

Transcriptional modulators are shown to be significant in differential activation/deactivation of genes, my question is considering recent advances in molecular biology have all the specific ...
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0answers
28 views

What are the enzymes with the lowest concentrations in a cell?

Or are there any enzymes which are only translated one time per cell?
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0answers
28 views

Do “real” human samples tend to return fewer protein identifications in Proteomics experiments?

I'm working with bottom-up (shotgun) mass spectrometry-based proteomics and have encountered an issue. If I do a run with a HeLa digest standard, the resulting data returns many protein IDs. When I do ...
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1answer
32 views

File sizes in Proteomics Experiments

I was wondering what file sizes does a typical proteomics experiment outputs in each phase (identification and quantification).| Also, how does the type of the quantification (relative, absolute) ...
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0answers
31 views

What's the best source characterizing proteolysis cleavage sites in the phagolysosome?

I have found MEROPS and TopFIND via the survey paper Quantitative proteomics and terminomics to elucidate the role of ubiquitination and proteolysis in adaptive immunity. These look like a good start, ...
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2answers
67 views

Get protein annotation from Uniprot out of protein mappings

Having a file of for about 10k mapping identifiers how can I get the annotations of the proteins from Uniprot ? As it is not possible to do It manually My mappings are contained in a .csv file They ...
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0answers
29 views

Get Network Out of proteins of interest

I have generated a list of Proteins using oncogeenes and suppressor genes of cancer. I have 5827 mapping identifier for 3916 interactions using STRINGdb R package . How do I build a network of 200k ...
5
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1answer
195 views

Where can I find large datasets of protein-interaction networks?

Where do I find large datasets of protein interaction networks for cancer or alzheimer diseases? So far, I found String but it is does not have enough proteins for my purposes. Are there such ...
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0answers
407 views

Why do my peptide samples turn yellow and red?

The protocols for (brain) tissue digestion I am trying out are: lysis (buffer containing 0.1% SDC or SDS in 100mM TEAB + phosphatase inhibitor which is sort of yellow), reduction with TCEP, alkylation ...
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1answer
47 views

Proteome patterns between treated and control cells

We did 4 experiments to compare the amount of certain proteins in treated and untreated cells. Each experiment was done separately. Because of the high cost of experiment, we were able to perform only ...
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1answer
114 views

Why is trypsin digestion required for proteomic studies? [closed]

I know that trypsin is used for proteomic studies, but I do not understand why trypsin digestion is necessary/important.
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2answers
1k views

Mass Spectrometry (proteomics): How isotopes can be used to to determine charge of the peaks?

I'm trying to understand how isotopes can tell me something about the charge of the different peaks. This pdf file mentioned the following about isotopes in correlation with the charge of the peaks: ...
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3answers
233 views

Genome and Proteome

Due to the dynamism of protein expression, a genome can give rise to different proteomes, but could we say that a proteome comes from different genomes?
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4answers
816 views

Bacterial cell lysis buffer used in proteomics procedures

What kinds of detergent-free bacterial lysis buffers exist? The proteins we're extracting will be later analyzed by LC-MS/MS, and we're looking for a lysis buffer that won't interfere with this ...