That sounds good. I was mostly worried I was doing the calculations wrong :)

Thanks!

My guess is that this is an issue of uncertainty and probably not a numerical issue. I'm fairly sure the numbers produced by the Molecules library are numerical...

When I generate average masses for peptides using this:


require 'molecules'

Molecules::Libraries::Residue['C'].mass {|e| e.std_atomic_weight.value }

=> 103.142...

As seen in BioRuby:

http://bioruby.org/rdoc/classes/...

Currently it's too difficult to remember and type full mappings in either form:

        "UniProtKB AC" => "UNIPROTACCS",
        "UniProtKB ID" => "UNIPROTI...

It sure would be nice if there were an established way to override just a few config parameters. Maybe generate a delegates hash and nest them?

TOPP does something similar and it's a good idea. While they make it happen by default, mspire could implement a separate task as a potential path in the analys...

Uniprot::Map and Pir::Map both could start failing on a dime and there's little helpful feedback.

For example, to set the default_blksize and carryover_limit.

Considering that is the more common line ending for HTTP exchanges.

• Check re multiple entries per value
• Check how modification sequences work when multiple modifications are at a single site