8 votes

Statistics: How are protein species distributed over cell types?

From my searches, there is no single resource that includes an atlas of all human proteins produced across all human cell types. However, there are several recent mass spectrometry studies that look ...
acvill's user avatar
  • 8,296
8 votes
Accepted

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

There is a bunch of decent protein-protein interaction databases: Biocarta, BioGrid, DIP, InnateDB, IntAct, MINT, PPID. Some of them aren't available now, but you can download datasets from the ...
Maxim Kuleshov's user avatar
5 votes

What happened to ProteomeCommons.org?

According to Lars Juhl Jensen on a Biostars forum, The Proteome Commons Tranche sadly shut down around 2013 due to lack of funding. It is a good example why important bioinformatics infrastructure ...
mgkrebbs's user avatar
  • 9,054
5 votes

How to find out what biological effects a molecule has, without having a specific mechanism or pathway in mind?

Personally I think this is a poor question, because the answer is immediately obvious to anyone who was worked with current technologies for both proteins and nucleic acids, but as always, it is hard ...
bob1's user avatar
  • 12.1k
4 votes

Are 'high-throughput' and 'large-scale' proteomics synonyms?

I often see the two terms used hand-in-hand, although I'd say they're not quite synonymous. Often the term high-throughput refers to the number of features being analyzed, with high-throughput methods ...
Nuclear Hoagie's user avatar
4 votes
Accepted

Peptide oxidation bias during sample preparation for LC-MS/MS

I know this was posted a long time ago and I'm not sure if you have found your answer but I am an author on two of the publications you andcite can offer some insight. 1.) Methionine oxidation, ...
John Bettinger's user avatar
4 votes

What happened to ProteomeCommons.org?

They seem to have lost the domain name. I believe all the data from that project is now on the UCSD site
De Novo's user avatar
  • 8,791
3 votes

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

I've changed the order of your questions so that the answers follow from one another. What do the isotopes have to do with the charge? The presence of isotopes has no effect on the charge of the ...
Michael_A's user avatar
  • 1,305
3 votes
Accepted

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

If you have an ion of mass 100 and charge 2, the m/z ratio (let's exclude the root) will be 100/2=50. If you have isotopes, then you expect to find several peaks for a given fragment. For example, the ...
alec_djinn's user avatar
  • 3,108
2 votes

Genome and Proteome

No, if you want to have a generally valid statement. You can not say: "that a proteome comes form different genomes". The official (MeSH) definition of the term "proteome" is: The protein complement ...
tsttst's user avatar
  • 1,597
2 votes
Accepted

Get protein annotation from Uniprot out of protein mappings

This problem is discussed here. Apparently STRING IDs are in KEGG format but these can be mapped on to Uniprot IDs using information downloadable from here. I guess that it is either the protein....
Alan Boyd's user avatar
  • 22.8k
2 votes
Accepted

How to integrate transcriptomics data with kinetic metabolic models?

I am assuming that in your model, the reactants and products (species) are metabolites and each reaction denotes conversion of one metabolite to another. From transcriptomics, you will get the ...
WYSIWYG's user avatar
  • 35.6k
2 votes

Average masses of atoms / amino acids

A bit more link following reveals on the UniMod site: "All mass values in Unimod are calculated from the IUPAC atomic weights and isotopic abundances tabulated by WebElements:" So, the ...
Armand's user avatar
  • 1,711
1 vote
Accepted

Does mass spectrometry data have units?

I think MS data, like other spectroscopy and chromatography data, is usually quantified by comparing peak areas (in arbitrary units) to those of a quantitative standard. So the Y axis is just the ...
Ryan's user avatar
  • 1,311
1 vote

Get protein annotation from Uniprot out of protein mappings

UniProt's batch download system, suggested by Alan Boyd above, also allows you to directly map identifiers, e.g. STRING to UniProtKB, or Ensembl to UniProtKB: http://www.uniprot.org/uploadlists Once ...
Elisabeth.Gasteiger's user avatar
1 vote
Accepted

Genome and Proteome

Yes, different genomes can produce the same proteome. Imagine a genome that only has a single protein-coding sequence (without splicing isoforms), the rest of the genome is simply regulatory ...
Armatus's user avatar
  • 7,660
1 vote

Genome and Proteome

Taking the first two answers into context, you cannot say given two proteomes that they came from different genomes, but as stated above in the first answer, if you consider a single base change to ...
FoldedChromatin's user avatar

Only top scored, non community-wiki answers of a minimum length are eligible