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Proteins of a particular size

I'm trying to learn how to search through protein mass spectra data and just finished reading through a nice guide at

http://www.ebi.ac.uk/pride/help/archive/search .

However, I'm still trying to learn how to accomplish a simple task. Specifically, I'd like to filter for protein sizes by looking only at small proteins/peptides with a specific number of amino acids. Does anyone have any good ideas on how to accomplish this?

proteomics proteins mass-spectroscopy
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updated by Ram Ram • written by dhbradshaw dhbradshaw

2 answers

Dear dhbradshaw,

Simply download your sequences in Excel format (if you're using UniProt let's say). Then open with Microsoft Excel and set "delimited importing" when it will ask you.

You will see the length of each protein on a specific column. Well then just order by number with excel option.

Greetings

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updated by Ram Ram • written by ilmagodellepcr • ilmagodellepcr

Thanks ilmagodellepcr.

So are you saying that if I want to filter for residue number then I need to download the sequences of every spectrum of interest?

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updated by Ram Ram • written by dhbradshaw dhbradshaw

einfo on protein: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=protein

tells us :

      <Field>
        <Name>MLWT</Name>
        <FullName>Molecular Weight</FullName>
        <Description>Molecular Weight</Description>
        <TermCount>364875</TermCount>
        <IsDate>N</IsDate>
        <IsNumerical>Y</IsNumerical>
        <SingleToken>Y</SingleToken>
        <Hierarchy>N</Hierarchy>
        <IsHidden>N</IsHidden>
      </Field>

So you can query NCBI protein with MLWT

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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Thanks Pierre.

If I understand you, this gives the molecular weight. What if what I want is the number of residues?

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updated by Ram Ram • written by dhbradshaw dhbradshaw

number of residues, it's the same:

		<field>
			<name>SLEN</name>
			<fullname>Sequence Length</fullname>
			<description>Length of sequence</description>
			<termcount>9635</termcount>
			<isdate>N</isdate>
			<isnumerical>Y</isnumerical>
			<singletoken>Y</singletoken>
			<hierarchy>N</hierarchy>
			<ishidden>N</ishidden>
		</field>
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written by Pierre Lindenbaum Pierre Lindenbaum

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