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```
In discussion with Lukas Kall, he pointed out to me that it appears mzid
appears to have limited support for capturing properties of peptide
identification (as opposed to PSMs). q-values, local …
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Dear Vadim,
>
> I have been trying to combine experimental library with prediction library for library search recently. The experimental library is named A, and four prediction libraries are nam…
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Hi everyone
I am new to FlashFLQ and I try to use it to quantify my proteomics data. The identification was done with sage and MS2 Rescore. I tried to generate the generic table for FlashLFQ with the…
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Hello,
I have my identifications in .mzIdentML format from a sulfo-SDA search on a single protein. Clicking on "map crosslinks" results in
Unique peptide pairs: 0 out of 0
Unique peptid…
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Hi @all: We have put one student analyzing the data to finish the project 🚀. We have made some major advances in the data analysis included in the following PR #55 in the results folder excel and figu…
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Hello, thank you for making EPIFANY, I am really excited to use it for my project. I am using EPIFANY to identify proteins from a idXML file converted from a Transition PQP file. However, the result r…
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Dear peptide-shaker team,
I receive this error when loading MSFragger result files :
> Sat Mar 09 23:03:26 CST 2024 Importing sequences from human_uniprot-proteome_UP000005640-2021.06.20.fa…
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Hi,
I am using DIAmeter for peptide identification from my data, in the original paper (https://academic.oup.com/bioinformatics/article/37/Supplement_1/i434/6319661) I found the mention of pepXML …
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> It would be nice to have one panel for each identified protein/s, with the peptide identifications showing the sequence coverage, at least when the protein sequence information is included in the m…
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I install MaxcotPercolator following https://www.sanger.ac.uk/science/tools/mascotpercolator. I try to run MascotPercolator on my Linux computer. However, it cannot work well and warn `No modifiaction…