Questions tagged [mass-spec]
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Mass spectrometry: What is meant by the 'most intense peptide ions' in data dependent acquisition (DDA) mode?
I am learning about data dependent acquisition (DDA) mode in mass spectrometry from this online resource. I have come across the following statement:
In DDA mode, the mass spectrometer selects the ...
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What are protein iBAQ abundance values in SWATH mass spectrometry?
I am reading a journal paper where they used SWATH mass spectrometry to quantify the abundance of proteins in synaptosomes isolated from different species. I am trying to determine whether some ...
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Does mass spectrometry data have units?
I am reading some journal papers about the proteome of certain brain structures. In these papers, they used mass spectrometry to identify the proteins that were present in the brain structure as well ...
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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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MS/MS for complex samples
I saw this figure in this atricle:
It's a really nice representation of what happens when using MS/MS. However I was wondering how this works when there are more proteins present in the gel spot. ...
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Are both B and Y ions required to determine the sequence of a protein by mass spectrometry?
I was wondering if both all b and y ions are required to determine to order of the amio acids in a peptide.
In my opinion knowing only ALL B ions or ALL y-ions is enough to determine the sequence of ...
user26290
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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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How do I tell whether a mass spectrum was made with ESI or MALDI?
I was working through a previous exam and came across the following question (with reference to the picture shown below):
"What MS ionization method was employed (MALDI or ESI)?"
I cannot seem to ...
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What makes the amide bond the lowest energy pathway? [closed]
I've reading about proteomics and how it can be used with mass spectrometry to sequence digested peptides.
Reading this paper the author states (in box 2):
peptide fragmentation induced by ...
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Mass Spectrometry Terminology
I began reading this paper (http://www.biomedcentral.com/1471-2105/14/56) and had a few questions about mass spectrometry terminology that I couldn't find answers to elsewhere. Consider the following ...
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Which mass spectrometry database search algorithms include the fragment mass accuracy in the calculation of protein scores?
E.g. in a MASCOT search, the accuracy of the fragment ions in a ms/ms spectrum does not have any influence on the scores of identified proteins (unless the fragment ions are out of the set ms/ms ...
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Mass change in deamidation from Glutamine to Glutamate
To detect the deamidation from Glutamine to Glutamate in a protein, normal practise seems to be a mass spec, where it is claimed there is a change of 1 dalton.
EG It is claimed that:
Deamidation ...
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