Protein sequences please help.

Question

[arjahejo]

How to find the molecular weight of protein by their sequences got from mass spectrometry experiment. Please suggest me good websites or technique, the specie is gallus gallus.

Answer 1

[Jean-Karim Heriche]

Most mass-spectrometry analysis software provide a report with the identified proteins. If for some reason, you can't/don't want to use this, you can do it yourself by aligning the peptides to a reference proteome. The trick is to apply the parsimony principle such that you find the minimal set of proteins that can explain the peptides present in your sample. See for example this paper on how to infer proteins from shotgun proteomics.

[arjahejo]

I have all sequences like this,

HSPA5 9031.ENSGALP00000001474 78 kDa glucose-regulated protein ; Probably plays a role in facilitating the assembly of multimeric protein complexes inside the ER (By similarity)

MRHLLLALLLLGGARADDEEKKEDVGTVVGIDLGTTYSCVGVFKNGRVEIIANDQGNRITPSYVAFTPEGERLIGDAAKNQLTSNPENTVFDAKRLIGRTWNDPSVQQDIKYLPFKVVEKKAKPHIQVDVGGGQTKTFAPEEISAMVLTKMKETAEAYLGKKVTHAVVTVPAYFNDAQRQATKDAGTIAGLNVMRIINEPTAAAIAYGLDKREGEKNILVFDLGGGTFDVSLLTIDNGVFEVVATNGDTHLGGEDFDQRVMEHFIKLYKKKTGKDVRKDNRAVQKLRREVEKAKRALSSQHQARIEIESFFEGEDFSETLTRAKFEELNMDLFRSTMKPVQKVLEDSDLKKSDIDEIVLVGGSTRIPKIQQLVKEFFNGKEPSRGINPDEAVAYGAAVQAGVLSGDQDTGDLVLLDVCPLTLGIETVGGVMTKLIPRNTVVPTKKSQIFSTASDNQPTVTIKVYEGERPLTKDNHLLGTFDLTGIPPAPRGVPQIEVTFEIDVNGILRVTAEDKGTGNKNKITITNDQNRLTPEEIERMVNDAEKFAEEDKKLKERIDARNELESYAYSLKNQIGDKEKLGGKLSSEDKETIEKAVEEKIEWLESHQDADIEDFKSKKKELEEVVQPIVSKLYGSAGPPPTGEEEAAEKDEL

How can i know molecular weight of this?

[Jean-Karim Heriche]

You already have the molecular weight in there. See this 78 kDa. That's a molecular weight. You could also compute it from the sequence using the weight of each amino-acid.

[arjahejo]

Its the only one, but I have other sequences as well where molecular weight is not mentioned. Like

YWHAB 9031.ENSGALP00000006578 14-3-3 protein beta/alpha ; Adapter protein implicated in the regulation of a large spectrum of both general and specialized signaling pathways. Binds to a large number of partners, usually by recognition of a phosphoserine or phosphothreonine motif. Binding generally results in the modulation of the activity of the binding partner (By similarity)

MDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTERNEKKQQMGREYREKIEAELQDICNDVLELLDKYLIVNATQPESKVFYLKMKGDYYRYLSEVASGDNKQTTVANSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACNLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN

[Jean-Karim Heriche]

So either compute it from the amino-acid molecular weights (there are tables such as this one) or use the Ensembl API to retrieve the molecular weights from the database.