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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 needs dedicated funding and should not have to operate out of research grants for individual groups.


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I think that the OP was asking about relevance of using urea with respect to the FASP method. In the FASP method, the primary denaturant is SDS . Protein are denatured with a ~4% SDS solution (buffered to pH 7.5 - 8.0). Then 8 M urea solution is used to replace the SDS. Urea serves two purposes here, first it keeps the protein denatured and in solutions as ...


4

It is a common practice to prove a result using an orthogonal technique. Like RNAseq followed by qRT-PCR etc. Western blotting is not a robust technique and cross comparisons are difficult because of difference in the avidities/affinities of different antibodies. So comparisons can be made only with one protein-control pair in different conditions. LC-MS ...


4

They seem to have lost the domain name. I believe all the data from that project is now on the UCSD site


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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, unlike cysteine oxidation, is irreversible without the action of a dedicated enzyme or catalyst. Neither TCEP nor DTT is able to reduce methionine sulfoxide. The ...


3

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 a high degree of confidence. So, they spiked known amounts of BSA, an extremely well-characterized protein frequently used in the lab, into their samples and ...


3

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 molecule. The physiochemical properties of the molecule and how the MS has been setup dictate how molecules acquire charges. This is important as methods ...


3

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 masses of different isotopes of the same molecule could be like: 100, 102, 105 and 107. In this case the spectrometer will detect four peaks, instead of one, ...


3

This is going to be a very long answer but to give a short response. You have to consider that MS for peptide detection works on the bases/principle of mass to charge (m/z) to detect an AA molecule, which is then normalised and analysed etc etc (http://en.wikipedia.org/wiki/Mass_spectrometry). Once you have the amino acids, then you just look at the order ...


2

8M urea is a denaturant, as @Chris mentioned. Denaturing proteins is important for molecular (aka classical) mass spectrometry. If you analyzed a non-denatured protein, you'd get information not only on the primary structure, but also on noncovalent interaction (2+°): The classical MS approach, so-called “molecular MS,” analyzes, in the gas phase of the ...


2

The original tests where done with blood and then: An eosinophillc index was calculated by multiplying the percentage of eosinophiles found in the routine white blood count by the total white blood count. An index of greater than 250 was considered positive. See table 8 in this paper: "Field evaluation of a respiratory syncytial virus vaccine and a ...


2

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 "phosphorylated" in their listing. It also appears to be possible to use NMR to study phosphorylated proteins. The situations where NMR/x-ray crystallography or ...


2

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 in a protein is much easier using mass spec. Detailed reasons: For X-ray you need to crystallize the protein which is often very difficult/impossible and ...


2

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, while the Peptide tool gives you the fragment ions of peptides. Modifications can easily attached to every site you want.


2

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 correctly. I will also assume that the peptide and protein identifications have been filtered to provide a false discovery rate of 1:100 at each level. You can ...


2

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 in hydrolysis and sample degradation ( also depends on the pH, neutral would be slower). Also you would have modifications to the amino acid side chains like ...


2

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 the machine is programmed to select the three most intense peaks (parent ions or precursor ions) from this scan for MS/MS (MS2). This process is repeated ...


2

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 science. Biological processes preferentially take up the lower mass isotope through kinetic fractionation. Via: https://en.wikipedia.org/wiki/Kinetic_fractionation ...


1

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 compound. This includes the PubChem Compound IDs that are given on the NCBI database. There are 2 265 compounds with LC-MS/MS spectra in the HMDB. The ...


1

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 be found here. I did a very quick and dirty comparison of the frequency that human ACSL_1 (Uniprot ID; P33121) and GAPDH were detected in control purifications. ...


1

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 the sequence. However, an MS/MS spectrum obtained from the mass spec instrument doesnt tell fragment types. Therefore it takes some expertise and tricks to spot ...


1

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.


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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.


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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 silico MS/MS fragmentation. There are other tools that attempt to accurately mimic the intensities of the various fragments that could be generated. The meaning ...


1

It is not simple MS, it is tandem MS. They send the sample through multiple MS and they fragment it between them. So they can get info about the molecular structure as well, not just the mass/charge of the molecule. A quote from your article: MS/MS spectra of the methylated H3 protein (top down) and fragments upon electron transfer dissociation ...


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