#209 lys-C gave trypsin-like digestion?

[Jeff Howbert]

I created a tide-index with --enzyme lys-c. The resulting peptides have extremely few examples with proline at the N-terminus. It appears a somewhat trypsin-like rule for C-terminal cleavage determinants [K]|{P} was used instead of lys-c [K]|[X].

Caveat: this index was created on 7/8/14. Current crux code base may have addressed this.

[Kaipo]

Is the lys-c cleavage rule not [K]|{P}? Comet and Mascot pages are consistent with that:
http://comet-ms.sourceforge.net/parameters/parameters_201402/search_enzyme_number.php
http://www.matrixscience.com/help/enzyme_help.html

The Mascot page does list an enzyme called "Lys-C/P" which does cleave as you described [K][X].

[William S Noble]

This problem could be addressed by explicitly listing the cleavage rules
for each of the enzymes in the tide-index.html documentation. E.g.,

• --enzyme <string> – Specify the enzyme used to digest the proteins in
  silico. Available enzymes (with the corresponding digestion rules
  indicated in parentheses) include no-enzyme ([X]|[X]), trypsin ([RK]|{P}),
  trypsin/p ([RK]|[X]), chymotrypsin, elastase, clostripain,
  cyanogen-bromide, iodosobenzoate, proline-endopeptidase, staph-protease,
  asp-n, lys-c, lys-n, arg-c, glu-c, pepsin-a, elastase-trypsin-chymotrypsin.
  Specifying --enzyme no-enzyme yields a non-enzymatic digest.Warning: the
  resulting index may be quite large. Default=trypsin.</string>

Kaipo, could you add the other rules in and check this change into SVN?

Bill

On Mon, Nov 10, 2014 at 1:06 PM, Kaipo kaipot@users.sf.net wrote:

Is the lys-c cleavage rule not [K]|{P}? Comet and Mascot pages are
consistent with that:

http://comet-ms.sourceforge.net/parameters/parameters_201402/search_enzyme_number.php
http://www.matrixscience.com/help/enzyme_help.html

The Mascot page does list an enzyme called "Lys-C/P" which does cleave as
you described [K][X].

---

• [issues:#209] http://sourceforge.net/p/cruxtoolkit/issues/209 lys-C
  gave trypsin-like digestion?*

Status: open
Milestone: post v2.0
Created: Mon Nov 10, 2014 08:57 PM UTC by Jeff Howbert
Last Updated: Mon Nov 10, 2014 08:57 PM UTC
Owner: nobody

I created a tide-index with --enzyme lys-c. The resulting peptides have
extremely few examples with proline at the N-terminus. It appears a
somewhat trypsin-like rule for C-terminal cleavage determinants [K]|{P}
was used instead of lys-c [K]|[X].

Caveat: this index was created on 7/8/14. Current crux code base may have
addressed this.

---

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[Jeff Howbert]

Hi Kaipo,

Ah ... I wasn't looking at the Comet or Mascot documentation. The online sources I had consulted (mostly enzyme vendor websites) say Lys-C is [K]|[X].

I did a little more digging. I found this publication in which a group of protein mass spectrometrists explored the question experimentally:

http://pubs.rsc.org/en/content/articlepdf/2010/cc/c0cc02523b

It's not black-and-white. Their results show Lys-C cleavage is impaired, but not prohibited, by proline on the C-terminal side of the cleavage site.

I guess it's best to leave our Lys-C definition as is (with the alternative Lys-C/P being available), but I wonder if we shouldn't add some clarifications to our documentation.

Jeff