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In processing metagenomics data sets, I would systematically avoid the use of the `-e` option, since we start from DNA reads (not peptides identified by mass spec). However, it seems that generally th…
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See the section "Reducing redundancy in proteomes" in the [UniProt april 2015 release notes](http://www.uniprot.org/help/2015/04/01/release) to find the explanation why the number of proteins in TrEMB…
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Dear All,
Today I run the philosopher v 1.4.4 with a custom formatted database (header line consists only of a unique identifier [made of letters, numbers and underscores], that is eventually prefx…
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Some proteins have a lot less peptides mapping to them than before. Example: P08238 (Heat shock protein HSP 90-beta (HS90B_HUMAN)) used to have 32 peptides, now it only has 10...
(Tested by loading…
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I am running SearchGUI-3.3.16 with 4 different search engines (X! Tandem, MS-GF+, OMSSA and Comet), my fasta file has around 140,000 entries and my spectrum file is around 60 MB. I am not running this…
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This is a question about how PepQuery handles isobaric substitutions. We search two different spectra files for the same peptide with the same protein reference database. PepQuery indicates that a spe…
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Hi,
Can the software do integration of the quantification data on the peptide level?
can I use it for middle and top down quantification? can it use isotopic envelopes of protein - either resolve…
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Several typos in the description. Here is the corrected text:
"During the peptide identification step, the search engine uses a decoy database to statistically access the quality of the peptide iden…
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Hi everyone,
Could somebody explain to me how the tool actually works, particularly the PEPMatrix algorithm?
I have read this article: https://www.ncbi.nlm.nih.gov/pubmed/21644507, but I still have …
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This thread serves as discussion forum for optimal parameter settings for search engine and quantification TOPP tools. Experimental data from different machines (Q Exactive, Q Star ...) will require d…