psidev-pi-dev — General Development List for Proteomics Informatics

[Psidev-pi-dev] Issue 53 in psi-pi: Encoding spectrum identifiers for MGF, PKL and DTA files

[<cod...@go...>]

Status: Accepted
Owner: dcreasy
Labels: Type-Defect Priority-Medium

New issue 53 by dcreasy: Encoding spectrum identifiers for MGF, PKL and DTA  
files
http://code.google.com/p/psi-pi/issues/detail?id=53

Section 5.1.4 of the specification states:

A <SpectrumIdentificationResult> is linked to the source spectrum (in an
external file) from which the identifications are made by way of a
reference in the spectrumID attribute and via the <SpectraData> element
which stores the URL of the file in the location attribute. It is
advantageous if there is a consistent system for identifying spectra in
different file formats. The following table is implemented in the PSI-MS CV
for providing consistent identifiers for different spectrum file formats:

...

MS:1000774	multiple peak list nativeID format:	
index=xsd:nonNegativeInteger	
Used for conversion of peak list files with multiple spectra, i.e. MGF,
PKL, merged DTA files. Index is the spectrum number in the file, starting
from 0.

 From the mzML doc for <spectrum id="">
The native identifier for a spectrum. For unmerged native spectra or
spectra from older open file formats, the format of the identifier is
defined in the PSI-MS CV and referred to in the mzML header. External
documents may use this identifier together with the mzML filename or
accession to reference a particular spectrum.

As discussed (at length!) here:
http://code.google.com/p/psi-pi/issues/detail?id=42#c37
it's not currently possible to write a converter for Mascot (and possibly
other search engines), to output this ID. Future releases of Mascot could
support this, but it won't help for older Mascot searches or other engines.
MGF files optionally contain other tags that could be used as described in
the reference above.


btw, we don't currently have MS:1000774 or any related term in any of the
examples which will make it pretty difficult for any importer to make
references back to the original raw data. So, I think that the mapping
needs to be changed to require a child of
MS:1000767 at the SpectraData/fileFormat level.

For reference:

[Term]
id: MS:1000767
name: native spectrum identifier format
def: "Describes how the native spectrum identifiers are formated." [PSI:MS]
synonym: "nativeID format" EXACT []
relationship: part_of MS:1000577 ! raw data file

If this is the case, we could (for Mascot) add another term:

[Term]
id: MS:100xxxxx
name: Mascot Query number
def: "index=xsd:nonNegativeInteger" [PSI:MS]
comment: The spectrum number in a Mascot results file, starting from 1.
is_a: MS:1000767 ! native spectrum identifier format

So, this would look like:

<SpectraData location="file:///est_coding_test.mgf" id="SD_1">
   <fileFormat>
     <cvParam accession="MS:1001062" name="Mascot MGF file" cvRef="PSI-MS" />
     <cvParam accession="MS:100xxxxx" name="Mascot Query number"
cvRef="PSI-MS" />
   </fileFormat>
</SpectraData>

And additionally, we can have:
   <SpectrumIdentificationResult id="query=1"
     <cvParam accession="MS:1000796" name="spectrum title" value="..."
cvRef="PSI-MS" />
     <cvParam accession="MS:1000797" name="peak list scans" value="..."
cvRef="PSI-MS" />
     <cvParam accession="MS:1000798" name="peak list raw scans" value="..."
cvRef="PSI-MS" />
     <cvParam accession="MS:1001114" name="retention time(s)" value="..."
cvRef="PSI-MS" />

(These 4 CV items are already present)

Trouble is, I can already hear howls of complaint from the mzML group with
the "query number" CV term.
Also, we need to determine what the other search engines can do and if a
term is required for them.

There's obviously no problem with the documentation or example for ids when
the input file was an mzML file.

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[Psidev-pi-dev] Schema update

[Jones, A. <And...@li...>]

Hi all,

I've uploaded candidate v1.0.0 versions of the XSDs to the SVN. Can everyone check that their examples validate okay against this version and that there's nothing I've missed moving this from "release candidate 1" to v1.0.0.

Before I upload the final spec document, a minor issue has come up about how we encode spectrum identifiers for MGF files (and possibly other input formats to search engines). It is difficult for some implementations (e.g. Mascot) to encode spectrumID as "index=1", since Mascot dat files do not store the index of the spectrum within the MGF file. This should not hold up v1 at all though, since I expect encoding policy things will come up as we go along. One option may be to discuss a mechanism for putting these minor policy updates on a webpage?

We will have a quick call to discuss this at 4pm tomorrow (13th Aug) UK time (http://www.timeanddate.com/worldclock/fixedtime.html?day=13&month=8&year=2009&hour=16&min=0&sec=0&p1=136)

Call agenda:


1.       Discuss encoding spectrumID

2.       Discuss status of implementations

3.       AOB (please send me agenda items)

Dial in details:

+ Germany: 08001012079
+ Switzerland: 0800000860
+ UK: 08081095644
+ USA: 1-866-314-3683
+ Generic international: +44 2083222500 (UK number)

access code: 297427

cheers
Andy



Schema Commit message:
**********************

Uploading candidate version 1.0.0 releases.

Changed the version number and mzIdentML element version regex.

Also deleted an empty <xsd:sequence/>

Added a minor documentation point to the MassTable (masses given are base masses not including fixed mods)

[Psidev-pi-dev] Issue 52 in psi-pi: numResidues is type xsd:int

[<cod...@go...>]

Updates:
	Status: Fixed
	Labels: Milestone-Release1.0

Comment #2 on issue 52 by eisenachM: numResidues is type xsd:int
http://code.google.com/p/psi-pi/issues/detail?id=52

(No comment was entered for this change.)

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Re: [Psidev-pi-dev] Resubmission of mzIdentML

[Jones, A. <And...@li...>]

Hi Norman,

Thanks for all your work helping to get the document through the process. Later today, I will update the documents so they say v1-release rather than v1-candidate.
Cheers
Andy

From: Norman Paton [mailto:no...@cs...]
Sent: 10 August 2009 09:48
To: Jones, Andy
Cc: 'Christian Stephan'; 'psi...@li...'
Subject: Re: Resubmission of mzIdentML


Your document has now completed its progress through the PSI standards process, and has been published as a PSI Final Document at: http://www.psidev.info/index.php?q=node/403.

Thank you for your work on behalf of the proteomics data standards community.

Regards, Norman

Jones, Andy wrote:
Dear PSI editors,
On behalf of the PI WG, I am re-submitting the mzIdentML specifications (formerly called AnalysisXML) to the PSI process as a candidate for version 1 final specifications, following reviewer comments. I have uploaded the specification document, XSDs, example files and readme to the PSI website:

http://www.psidev.info/index.php?q=node/403

I have also attached our responses to anonymous reviewers and comments received on the mailing list during the public comment phase.
Best wishes,
Andy

Re: [Psidev-pi-dev] Resubmission of mzIdentML

[Norman P. <no...@cs...>]

Your document has now completed its progress through the PSI standards 
process, and has been published as a PSI Final Document at: 
http://www.psidev.info/index.php?q=node/403.

Thank you for your work on behalf of the proteomics data standards 
community.

Regards, Norman

Jones, Andy wrote:
>
> Dear PSI editors,
>
> On behalf of the PI WG, I am re-submitting the mzIdentML 
> specifications (formerly called AnalysisXML) to the PSI process as a 
> candidate for version 1 final specifications, following reviewer 
> comments. I have uploaded the specification document, XSDs, example 
> files and readme to the PSI website:
>
>  
>
> http://www.psidev.info/index.php?q=node/403
>
>  
>
> I have also attached our responses to anonymous reviewers and comments 
> received on the mailing list during the public comment phase.
>
> Best wishes,
>
> Andy
>
>  
>
>  
>

[Psidev-pi-dev] Issue 52 in psi-pi: numResidues is type xsd:int

[<cod...@go...>]

Comment #1 on issue 52 by andrewrobertjones: numResidues is type xsd:int
http://code.google.com/p/psi-pi/issues/detail?id=52

Thanks for pointing this out - now fixed:

Changed numResidues numDatabaseSequences and numSequencesSearched from  
xsd:int to
xsd:long

I don't know if the latter two changes are required but people might  
plausibly search
massive databases in the future


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[Psidev-pi-dev] Issue 52 in psi-pi: numResidues is type xsd:int

[<cod...@go...>]

Status: New
Owner: ----
Labels: Type-Defect Priority-Medium

New issue 52 by jcottr...@matrixscience.com: numResidues is type xsd:int
http://code.google.com/p/psi-pi/issues/detail?id=52

/mzIdentML/DataCollection/Inputs/SearchDatabase/@numResidues is type
xsd:int, which is a problem, because some databases have more than 2
billion residues.


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[Psidev-pi-dev] Issue 44 in psi-pi: Issues with all instance docs

[<cod...@go...>]

Comment #27 on issue 44 by dcreasy: Issues with all instance docs
http://code.google.com/p/psi-pi/issues/detail?id=44

Regarding comment 26: Mascot example changed.

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[Psidev-pi-dev] Specification document

[Jones, A. <And...@li...>]

Hi all,

Eric very kindly fixed the auto-generated specifications so I’ve folded these into main spec doc and performed a few other fixes. I also noticed one or two missing pieces of documentation that I’ve updated in the schema and the spec doc.

http://code.google.com/p/psi-pi/source/browse/trunk/specification_document/mzIdentML_releaseCandidate1.doc

I think this doc is now ready to go back into the process. If anyone wants to have a final look over the weekend, let me know if you spot anything, then I’ll submit on Monday.
Cheers
Andy

[Psidev-pi-dev] Issue 44 in psi-pi: Issues with all instance docs

[<cod...@go...>]

Comment #26 on issue 44 by andrewrobertjones: Issues with all instance docs
http://code.google.com/p/psi-pi/issues/detail?id=44

Some minor fixes needed to instance docs prior to submission:

MPCExample (remove this line)
	<!-- CAUTION: ALL experimentalMassToCharge, peptide scores, protein scores  
and
sequence coverage values are only placeholders for the real values, because  
file is
handcrafted and shows only principle structure of AnalysisXML! -->


Mascot MS/MS example:
<userParam name="Mascot User Comment" value="Example Mascot MS-MS search  
for PSI
AnalysisXML"/>

If Martin is away, I'll manually fix the MPC example for now


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[Psidev-pi-dev] Minor fixes to instance docs

[Jones, A. <And...@li...>]

Updates to the issues list don't seem to be getting forwarded to the list... so I'll send manually.
Cheers
Andy



Some minor fixes needed to instance docs prior to submission:

MPCExample (remove this line)
                <!-- CAUTION: ALL experimentalMassToCharge, peptide scores, protein scores and
sequence coverage values are only placeholders for the real values, because file is
handcrafted and shows only principle structure of AnalysisXML! -->


Mascot MS/MS example:
<userParam name="Mascot User Comment" value="Example Mascot MS-MS search for PSI
AnalysisXML"/>

Re: [Psidev-pi-dev] proteowizard mzIdentML usage example available.

[Robert B. <rob...@pr...>]

Ok, we're still working out the last of the cv issues, but I believe it
should produce valid mzIdentML in the general case.

On Thu, Jul 23, 2009 at 5:29 AM, David Creasy <dc...@ma...>wrote:

>  Hello Rob,
>
> That's great. Looks like there are a few validation issues (apart from the
> internal references) that need to be fixed. hopefully you are aware of the
> validator here:
>
> http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/analysisXML/index.php
>
> Thanks,
>
> David
>
>
> Robert Burke wrote:
>
> Hello everyone,
>
> Proteowizard's MzIdentML package can now generate MzIdentML files. Our
> example output can be found at
> http://proteowizard.sourceforge.net/example_data/tiny.pwiz.mzid . It was
> generated by the
> proteowizard/pwiz_tools/examples/write_mzid_example_files.cpp program.
> Reading and internal references resolution are coming soon.
>
> -RB
>
>
> ------------------------------
>
> ------------------------------------------------------------------------------
>
>
> ------------------------------
>
> _______________________________________________
> Psidev-pi-dev mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
>
>
> --
> David Creasy
> Matrix Science
> 64 Baker Street
> London W1U 7GB, UK
> Tel: +44 (0)20 7486 1050
> Fax: +44 (0)20 7224 1344
> dc...@ma...http://www.matrixscience.com
>
> Matrix Science Ltd. is registered in England and Wales
> Company number 3533898
>
>

Re: [Psidev-pi-dev] Spec doc

[Jones, A. <And...@li...>]

Hi all,
Quick update on the spec document. Thanks to everyone who has commented so far. I won’t have time to go through it and submit till around Wed next week unfortunately, so if anyone else would like to proof read and comment before Tues, it would be much appreciated,
Cheers
Andy



From: Jones, Andy [mailto:And...@li...]
Sent: 23 July 2009 15:39
To: 'psi...@li...'
Subject: Re: [Psidev-pi-dev] Spec doc

Hi all,
Just to confirm, there will not be a call today,
Cheers
Andy

From: Jones, Andy [mailto:And...@li...]
Sent: 22 July 2009 16:11
To: 'psi...@li...'
Subject: Re: [Psidev-pi-dev] Spec doc

Hi all,

We had scheduled a conference call for tomorrow afternoon. At the moment, the main outstanding task seems to be reviewing the spec document, so we may not need a call. If anyone would like to discuss any open issues, give me a mail and we’ll hold a brief call tomorrow,
Cheers
Andy

From: Jones, Andy [mailto:And...@li...]
Sent: 21 July 2009 13:41
To: 'psi...@li...'
Subject: [Psidev-pi-dev] Spec doc

Hi all,

The draft of the specification document has been re-generated and is in the SVN and directly linked here:

http://code.google.com/p/psi-pi/source/browse/trunk/specification_document/mzIdentML_releaseCandidate1.doc

I’m hoping to submit this to the doc process by the end of Friday so can everyone review this carefully. I’ve picked up one or two things in the auto-generation process that need to be fixed (e.g. remove “pf:” throughout), but I think we can fix these with find and replace.

I don’t have much time to look at this for a couple of days but I thought I’d get it out now to give everyone as much time as possible for review. Please send minor fixes to me directly or issues for discussion can be posted in a new issue: http://code.google.com/p/psi-pi/issues/detail?id=51

Cheers
Andy

[Psidev-pi-dev] Issue 51 in psi-pi: Issues with the spec doc

[<cod...@go...>]

Comment #6 on issue 51 by dcreasy: Issues with the spec doc
http://code.google.com/p/psi-pi/issues/detail?id=51

The example for Sample doesn't show the use of sub samples. The only one  
that does
this is the 15N example - could maybe swap it for that one?

7.6 Database Filter
Example needs updating from Mascot 15N example
The paragraph after the example is no longer correct. Can probably just be  
removed?

7.7 Do we still have any <ParamType>?


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[Psidev-pi-dev] Issue 51 in psi-pi: Issues with the spec doc

[<cod...@go...>]

Comment #5 on issue 51 by eisenachM: Issues with the spec doc
http://code.google.com/p/psi-pi/issues/detail?id=51

It seems that there are some elements missing in the automatically  
generated part of
the schema desription, e.g.:

<Measure>
<SpectrumIdentificationItem>
<ProteinDetectionHypothesis>
<PeptideEvidence>
<Fragmentation>
<PeptideHypothesis>
<IonType>
<FragmentArray>

In the AnalysisXML spec doc these were listed after <Exclude>, which is  
here the last
described element.

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[Psidev-pi-dev] Issue 51 in psi-pi: Issues with the spec doc

[<cod...@go...>]

Comment #4 on issue 51 by eisenachM: Issues with the spec doc
http://code.google.com/p/psi-pi/issues/detail?id=51

A "graphical context" paragraph is missing for element <mzIdentML>, for  
which I
grabbed an image, but not include

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[Psidev-pi-dev] Issue 51 in psi-pi: Issues with the spec doc

[<cod...@go...>]

Updates:
	Labels: Milestone-Release1.0

Comment #3 on issue 51 by eisenachM: Issues with the spec doc
http://code.google.com/p/psi-pi/issues/detail?id=51

A section about the element <SpectrumIdentificationItem> is missing, as  
well as its
graphical context, which I have grabbed, but could not include.

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Re: [Psidev-pi-dev] Spec doc

[Jones, A. <And...@li...>]

Hi all,
Just to confirm, there will not be a call today,
Cheers
Andy

From: Jones, Andy [mailto:And...@li...]
Sent: 22 July 2009 16:11
To: 'psi...@li...'
Subject: Re: [Psidev-pi-dev] Spec doc

Hi all,

We had scheduled a conference call for tomorrow afternoon. At the moment, the main outstanding task seems to be reviewing the spec document, so we may not need a call. If anyone would like to discuss any open issues, give me a mail and we’ll hold a brief call tomorrow,
Cheers
Andy

From: Jones, Andy [mailto:And...@li...]
Sent: 21 July 2009 13:41
To: 'psi...@li...'
Subject: [Psidev-pi-dev] Spec doc

Hi all,

The draft of the specification document has been re-generated and is in the SVN and directly linked here:

http://code.google.com/p/psi-pi/source/browse/trunk/specification_document/mzIdentML_releaseCandidate1.doc

I’m hoping to submit this to the doc process by the end of Friday so can everyone review this carefully. I’ve picked up one or two things in the auto-generation process that need to be fixed (e.g. remove “pf:” throughout), but I think we can fix these with find and replace.

I don’t have much time to look at this for a couple of days but I thought I’d get it out now to give everyone as much time as possible for review. Please send minor fixes to me directly or issues for discussion can be posted in a new issue: http://code.google.com/p/psi-pi/issues/detail?id=51

Cheers
Andy

Re: [Psidev-pi-dev] proteowizard mzIdentML usage example available.

[Robert B. <rob...@pr...>]

Thank you David,



On Thu, Jul 23, 2009 at 5:29 AM, David Creasy <dc...@ma...>wrote:

>  Hello Rob,
>
> That's great. Looks like there are a few validation issues (apart from the
> internal references) that need to be fixed. hopefully you are aware of the
> validator here:
>
> http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/analysisXML/index.php
>
> Thanks,
>
> David
>
>
> Robert Burke wrote:
>
> Hello everyone,
>
> Proteowizard's MzIdentML package can now generate MzIdentML files. Our
> example output can be found at
> http://proteowizard.sourceforge.net/example_data/tiny.pwiz.mzid . It was
> generated by the
> proteowizard/pwiz_tools/examples/write_mzid_example_files.cpp program.
> Reading and internal references resolution are coming soon.
>
> -RB
>
>
> ------------------------------
>
> ------------------------------------------------------------------------------
>
>
> ------------------------------
>
> _______________________________________________
> Psidev-pi-dev mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
>
>
> --
> David Creasy
> Matrix Science
> 64 Baker Street
> London W1U 7GB, UK
> Tel: +44 (0)20 7486 1050
> Fax: +44 (0)20 7224 1344
> dc...@ma...http://www.matrixscience.com
>
> Matrix Science Ltd. is registered in England and Wales
> Company number 3533898
>
>

Re: [Psidev-pi-dev] proteowizard mzIdentML usage example available.

[David C. <dc...@ma...>]

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
  <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
  <title></title>
</head>
<body bgcolor="#ffffff" text="#000000">
Hello Rob,<br>
<br>
That's great. Looks like there are a few validation issues (apart from
the internal references) that need to be fixed. hopefully you are aware
of the validator here: <br>
<a class="moz-txt-link-freetext" href="http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/analysisXML/index.php">http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/analysisXML/index.php</a><br>
<br>
Thanks,<br>
<br>
David<br>
<br>
<br>
Robert Burke wrote:
<blockquote
 cite="mid:f5b...@ma..."
 type="cite">Hello everyone,<br>
  <br>
Proteowizard's MzIdentML package can now generate MzIdentML files. Our
example output can be found at <a moz-do-not-send="true"
 href="http://proteowizard.sourceforge.net/example_data/tiny.pwiz.mzid">http://proteowizard.sourceforge.net/example_data/tiny.pwiz.mzid</a>
. It was generated by the
proteowizard/pwiz_tools/examples/write_mzid_example_files.cpp program.
Reading and internal references resolution are coming soon.<br>
  <br>
-RB<br>
  <br>
  <br>
  <pre wrap="">
<hr size="4" width="90%">
------------------------------------------------------------------------------
  </pre>
  <pre wrap="">
<hr size="4" width="90%">
_______________________________________________
Psidev-pi-dev mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Psi...@li...">Psi...@li...</a>
<a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev">https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev</a>
  </pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">-- 
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344

<a class="moz-txt-link-abbreviated" href="mailto:dc...@ma...">dc...@ma...</a>
<a class="moz-txt-link-freetext" href="http://www.matrixscience.com">http://www.matrixscience.com</a>

Matrix Science Ltd. is registered in England and Wales
Company number 3533898</pre>
</body>
</html>

[Psidev-pi-dev] proteowizard mzIdentML usage example available.

[Robert B. <rob...@pr...>]

Hello everyone,

Proteowizard's MzIdentML package can now generate MzIdentML files. Our
example output can be found at
http://proteowizard.sourceforge.net/example_data/tiny.pwiz.mzid . It was
generated by the
proteowizard/pwiz_tools/examples/write_mzid_example_files.cpp program.
Reading and internal references resolution are coming soon.

-RB

Re: [Psidev-pi-dev] Specifying protein termini in cleavage agent regexes

[David C. <dc...@ma...>]

Hi Matt,

http://code.google.com/p/psi-pi/issues/detail?id=30&can=1&q=regex#c9
and
http://code.google.com/p/psi-pi/issues/detail?id=30&can=1&q=regex#c20

describe how to check this in perl/java.

  $protein = "MABCDKPEFGHIJKLMNOPQRSTUVWXYZ";
  @peptides = split(/(?<=^M)|(?<=[KR])(?!P)/, $protein);
  print join "\n", @peptides;

gives:

M
ABCDKPEFGHIJK
LMNOPQR
STUVWXYZ

which may not be what you intend because it doesn't also give:
MABCDKPEFGHIJK

However, I'm not sure that it's really right to add this to the enzyme 
definition unless this is how your software really works? Doesn't seem 
quite the right place to me...

David

Matthew Chambers wrote:
> Nevermind I think. Would something like (?<=^M)|(?<=[KR])(?!P) work?
> 
> -Matt
> 
> 
> Matthew Chambers wrote:
>> Hi all,
>>
>> It's a reasonable assumption that the protein termini are valid cleavage 
>> sites for all agents, but is at least one special case where some 
>> representation for the protein terminus is necessary: in silico clipping 
>> of n-terminal methionine. How can that rule be represented in a regex? 
>> In the pwiz digestion motif, trypsin with n-terminal M clipping would be 
>> two rules, "{M|" and "[KR]|[^P]". The '{' represents the protein 
>> n-terminus. In regex form this might look like: (?<={M)|(?<=[KR])(?!P) 
>> but as you can see it still requires a special character for the terminus.
>>
>> Thoughts?
>> -Matt
>>
>>   
> 
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Re: [Psidev-pi-dev] Specifying protein termini in cleavage agent regexes

[Matthew C. <mat...@va...>]

Nevermind I think. Would something like (?<=^M)|(?<=[KR])(?!P) work?

-Matt


Matthew Chambers wrote:
> Hi all,
>
> It's a reasonable assumption that the protein termini are valid cleavage 
> sites for all agents, but is at least one special case where some 
> representation for the protein terminus is necessary: in silico clipping 
> of n-terminal methionine. How can that rule be represented in a regex? 
> In the pwiz digestion motif, trypsin with n-terminal M clipping would be 
> two rules, "{M|" and "[KR]|[^P]". The '{' represents the protein 
> n-terminus. In regex form this might look like: (?<={M)|(?<=[KR])(?!P) 
> but as you can see it still requires a special character for the terminus.
>
> Thoughts?
> -Matt
>
>   

[Psidev-pi-dev] Specifying protein termini in cleavage agent regexes

[Matthew C. <mat...@va...>]

Hi all,

It's a reasonable assumption that the protein termini are valid cleavage 
sites for all agents, but is at least one special case where some 
representation for the protein terminus is necessary: in silico clipping 
of n-terminal methionine. How can that rule be represented in a regex? 
In the pwiz digestion motif, trypsin with n-terminal M clipping would be 
two rules, "{M|" and "[KR]|[^P]". The '{' represents the protein 
n-terminus. In regex form this might look like: (?<={M)|(?<=[KR])(?!P) 
but as you can see it still requires a special character for the terminus.

Thoughts?
-Matt

Re: [Psidev-pi-dev] Spec doc

[Jones, A. <And...@li...>]

Hi all,

We had scheduled a conference call for tomorrow afternoon. At the moment, the main outstanding task seems to be reviewing the spec document, so we may not need a call. If anyone would like to discuss any open issues, give me a mail and we’ll hold a brief call tomorrow,
Cheers
Andy

From: Jones, Andy [mailto:And...@li...]
Sent: 21 July 2009 13:41
To: 'psi...@li...'
Subject: [Psidev-pi-dev] Spec doc

Hi all,

The draft of the specification document has been re-generated and is in the SVN and directly linked here:

http://code.google.com/p/psi-pi/source/browse/trunk/specification_document/mzIdentML_releaseCandidate1.doc

I’m hoping to submit this to the doc process by the end of Friday so can everyone review this carefully. I’ve picked up one or two things in the auto-generation process that need to be fixed (e.g. remove “pf:” throughout), but I think we can fix these with find and replace.

I don’t have much time to look at this for a couple of days but I thought I’d get it out now to give everyone as much time as possible for review. Please send minor fixes to me directly or issues for discussion can be posted in a new issue: http://code.google.com/p/psi-pi/issues/detail?id=51

Cheers
Andy