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
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
Accepted

Why bovine serum albumin is used in mass-spectroscopy and how to interpret such data?

Their LC-MS-MS data was only semi-quantitative as gathered, meaning they could compare relative levels of one protein to another in the same sample, but not necessarily between different samples with ...
MattDMo's user avatar
  • 15.3k
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

Techniques for detecting phosphorylation sites in proteins?

X-ray crystallography has been used to detect phosphorylated sites. The RCSB protein database currently contains 856 structures that have both a resolution below 3 angstroms and the keyword "...
Michael_A's user avatar
  • 1,305
2 votes
Accepted

Techniques for detecting phosphorylation sites in proteins?

In principle X-ray crystallography or NMR could detect phosphorylation sites but they are much more complex and expensive techniques than mass spec. So for simply figuring out phosphorylation patterns ...
Thawn's user avatar
  • 1,239
2 votes

How to generate simulated mass-spectrometry data for phosphorylated proteins?

I know this is a two years old question... but I recently developed a web application which could be useful for you: Prot pi The Protein tool lets you simulate the mass spectrum of the intact protein,...
roland's user avatar
  • 121
2 votes
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What is the best way to analyze non-quantitative mass spec hits from an immunoprecipitation pull down?

If they are available, talk to the people who analysed your data. Using their knowledge is intelligent. I will assume two critical steps are completed. First that your results have been searched ...
Michael_A's user avatar
  • 1,305
2 votes

Can I dry digested protein sample over weekend in a vacuum concentrator?

If your sample dried in the speed-vac then it should not cause to much damage to the sample. But if Speed Vac stopped and there was some liquid left, then incubation at room temperature would result ...
ktyagi's user avatar
  • 261
2 votes
Accepted

MS/MS for complex samples

Liquid chromatography (LC) allows the peptides from a complex sample to be fed into the mass spectrometer over time. The bottom half of the image shows an MS spectrum from a single precursor scan and ...
Michael_A's user avatar
  • 1,305
2 votes
Accepted

How do carbon 13:12 ratios confirm the biological origin of oldest microfossils?

Via: https://en.wikipedia.org/wiki/Carbon-13#Uses_in_science Due to differential uptake in plants as well as marine carbonates of 13C, it is possible to use these isotopic signatures in earth ...
Alex Reynolds's user avatar
2 votes

Identifying substance in body fluid (serum, urine)

Dipstick urinalysis? source The urine dipstick has a bunch of squares, each with a chemical analysis ready to go. The dip will semiquantitatively show you what is in the urine. My bet would be ...
Willk's user avatar
  • 2,964
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
Accepted

Open Mass Spec Database

The Human metabolome database (HMDB) contains many MS/MS and NMR spectra for human metabolites. You can acquire the spectra from the downloads section. The HMDB includes external identifiers for each ...
Michael_A's user avatar
  • 1,305
1 vote

False positives in TAP - MS experiments

The common repository for affinity purification (CRAPome) contains the results from many tandem affinity experiments and scores them based on their presence in control purifications. The database can ...
Michael_A's user avatar
  • 1,305
1 vote

Are both B and Y ions required to determine the sequence of a protein by mass spectrometry?

In an MS/MS spectrum, difference between the successive peaks of a b or y ion series allows one to determine the amino acids making the series/peptide. Either one of them should be enough to give you ...
ktyagi's user avatar
  • 261
1 vote

Transfer of electrophoresis bands to MS

You have to remove the salts, remove the dye, digest the protein, extract the digested peptides from the gel etc. For details, see this protocol.
WYSIWYG's user avatar
  • 35.6k
1 vote

How to generate simulated mass-spectrometry data for phosphorylated proteins?

Have a look at PeptideMass, you can choose to use the "post-translational modifications" option that will output the masses of phosphorylated (among other modifications) peptides.
alec_djinn's user avatar
  • 3,108
1 vote

How to generate simulated mass-spectrometry data for phosphorylated proteins?

For peptides (bottom up) mMass accepts a sequence of interest and phosphorylated tyrosine can be specified as a modification after that. The program also performs in silico enzyme digests and in ...
Michael_A's user avatar
  • 1,305

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