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SILAC (Stable Isotope Labeling by Amino acids in Cell culture) can be used to detect
features (typically PTMs) required for a given interaction - see, for example PMID: 2223140
The method is differen…
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```
Hi.
I use peptide shaker to (in addition to "normal" proteomics) to also search my
standard synthetic peptides and other known small peptides not necessary from
proteins. I do this by adding th…
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```
> What steps will reproduce the problem?
> What is the expected output? What do you see instead?
> What version of the product are you using? On what operating system?
Version 0.38.2 on Window…
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```
> What steps will reproduce the problem?
data import
> What is the expected output? What do you see instead?
identified proteins/PTMs
> What version of the product are you using? On what operati…
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Jimmy Eng:
Update https://github.com/percolator/percolator/wiki/Interface with a description of PTM annotation.
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My Peptide Shaker imports typically fail (think even always) when switching off the the "Probabilistic Scoring" in the PTM Scoring module. Is that expected? The step takes really long in my hands (app…
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This is an improvement suggestion...
It seems that you are using some binary format to store the parameters of search GUI.
I can't see a reason for this type of format when the file is just 10K.
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```
Dear All,
I found the comnination of SeachGui and PeptideShaker very useful, althou
sometimes I observe crashes or errors. Usually rerunning helps to resolve the
problems.
By trying to import …
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The output of tide-search (inside the crux toolkit) writes PTMs in the sqt output as `A.PEPT[80]ID.E` (here a phosphorylation), this causes a parsing error in sqt2pin, which expects PTMs to be formatt…
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```
> What steps will reproduce the problem?
Importing 10 fractions searched with 7 search engines appears to import and
process fine until it reaches: "Validating identifications at 1% FDR, quality …