Peptide MS Peak Width

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woa
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Peptide MS Peak Width

Postby woa » Thu Jan 09, 2014 11:54 am

Hello,

I'm urgently looking for a software/library to find the MS peak width of the identified peptide.
Can anybody help ? I've access to Mascot 2.3 , ProteomeDiscoverer 1.3 and 1.4 , Peaks etc.
Thanks in advance

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Doug
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Postby Doug » Thu Jan 09, 2014 3:18 pm

woa, I have a couple of questions regarding exactly what you need.

1) Are you interested in the width of the peak in the MS1 spectrum (in m/z) or the width of the elution peak (in seconds)?

2) What throughput do you need? Just a few (1-10 peptides)? Or all identified peptides?
"If we knew what we were doing it wouldn't be research." -AE

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Postby Craig » Thu Jan 09, 2014 4:09 pm

If you need high throughput, you could try either NIST MSQC or QuaMeter from David Tabb's group. Both of these calculate the CPTAC metrics which include peak width.

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Postby woa » Thu Jan 09, 2014 10:16 pm

Thanks all for your answers. Doug, I'm interested in the MS1 spectrum peak. I wish to get the peaks for all identified peptides, typically a couple of thousands, obtained from a QXactive

I'll have a look into the software you mentioned Craig.

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Postby Craig » Fri Jan 10, 2014 9:26 am

Also, you are probably aware of this, but Qual Browser (at least the last version I used) will report MS peak widths. So you could check peaks at various m/z's. The widths should be stable throughout the entire run, so it's probably not necessary to check all of the thousands of peptides you identified.

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Postby Infinity » Mon Jan 13, 2014 12:10 pm

What you need is MaxQuant, there is an option called "calculate peak properties" which will give you not just peak width but lot's of other related parameters (in a separate txt file).

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Postby woa » Mon Jan 13, 2014 1:48 pm

Thanks all,

I need to find out the width of the Elution peak as well. Doug, do you have any suggestions? Infinity, can Maxquant report that too?

Thanks

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Doug
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Postby Doug » Mon Jan 13, 2014 1:58 pm

Woa, I don't have any suggestion in particular. I was only asking for clarification since it might help others understand your question. But my guess is that MaxQuant will report the chromatographic peak width as well.

Good luck. Tell us what ends up working for you.
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Postby woa » Mon Jan 13, 2014 2:04 pm

I've noted that Skyline can report "MaxFwhm*–*The*maximum*full*width*at*half*max*(FWHM)*of*the*transitions*for*the*precursor" under the "PrecursorResults" result export menu. I guess that won't be of any help for me, or will it be?

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Postby Infinity » Tue Jan 14, 2014 11:58 am

In MaxQuant (output file "allPeptides.txt") you will get the following peak-shape parameters:
Retention Time,
Retention Length,
Retention Length (FWHM)

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Postby woa » Tue Jan 14, 2014 7:57 pm

Thanks Infinity,
I too noted that The "AllPeptides.txt" file contains that information under the "Retention Length (FWHM)" column. However I'm having
problem to connect this information with identified peptides. I can't find any field through which I can connect it to the peptide data.
For example how to connect the AllPeptides fields(http://pastebin.com/TtHjJanv) to that of 'Peptides.txt' fields(http://pastebin.com/4SZCbpJw)
Can you help?
thanks

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Postby Infinity » Wed Jan 15, 2014 10:25 am

Yep, they do not have some kind of unique id that you can use. I would try combination of m/z value and retention time to find corresponding peptides. But be careful, each entry in Peptides.txt represents peak which is not necessary belongs to particular peptides (e.g. there are lots of entries with z=+1, that are typically not even sequenced by MS/MS). Also many peptides could be represented by several entries in Peptides.txt (like different charged forms, or modified with different PTMs).

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Postby achimt » Wed Jan 15, 2014 2:32 pm

woa,

I think there might be a way of getting from the AllPeptides fields to the identifications and that is through the 'scans' field. If you retain the scan number of an MSMS spectrum in the *.mgf peaklist file (you can do this using msconvert), it can get carried over to X!Tandem results in the BioML format. From that you can the extract the scan number in a table per identified peptide and compare it to the scan numbers in the AllPeptides table.

I might have a couple of python scripts that would help you with doing that. Let me know, if you want them.

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Postby woa » Fri Jan 17, 2014 11:11 am

^ Thnaks AchimT. It would be great if you can send me the Python Scripts. I've messaged my email Id to you. Otherwise you can post it in eg. pastebin, and share the link here.

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Postby Kelstrup » Tue Jan 28, 2014 5:54 am

If you have questions on MaxQuant you could try the Google group that exists for this purpose:
http://groups.google.com/group/maxquant-list

cheers

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Postby woa » Wed Jan 29, 2014 11:55 am

Yes already posted it on 14th Jan. in MQ discussin group.
https://groups.google.com/forum/#!topic/maxquant-list/LPQOQMVjn9k

The reply I got is as follows:
"hi
this is a known nagging issue and is resolved in the next released. current workaround is to use the evidence table where this information should be written out as retention length. (however from base to base and not FWHM)"

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Postby woa » Thu Feb 06, 2014 8:47 am

I finally solved the problem using the Multiplierz program. Available from http://blais.dfci.harvard.edu/index.php?id=63


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