Proteins of a particular size

Question

[dhbradshaw]

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?

Answer 1

[ilmagodellepcr]

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

[Pierre Lindenbaum]

[dhbradshaw]

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?

Answer 2

[Pierre Lindenbaum]

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

[dhbradshaw]

Thanks Pierre.

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

[Pierre Lindenbaum]

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>