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Hello Fengchao and others on the IonQuant team,
Using Fragpipe, I am searching for modified peptides with the labile/detailed mass-offset search and quantifying with IonQuant. I have one fixed modi…
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_**Case 1: Inserting the fragment below CHEM structure with R1-R1, R2-R2 bonds**_
**Steps to Reproduce**
1. Open two Ketcher browser tabs – the Macro mode
2. Open this file (first unzip) [CHEM R…
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Hello, I want to use DEqMS to analyze my LFQ dataset, which consists of five samples (each in triplicate) and analyze the DEPS among all ten possible comparison pairs. Should I use the values from the…
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Hello,
we have generated an HLA-peptides library using PeptDeep-HLA for the prediction of peptides and alphapeptdeep for library generation and conversion to .tsv for compatibility with DIANN. Then…
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Dear colleagues,
It would be very helpful to have example files to work with progenesis.
Particularly the peptides file (does it have to be .txt?) and annotation file.
Àlex Bayés
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Is there a way to specify the minimum or maximum peptide length for a search? I noticed that the default value for minimum peptide length is 6 from the output .pglyco file but couldn't find a way to m…
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@dfermin:
I'm doing some analysis here and I found that when `decoys` are not exported some of the peptides in the input are not exported, but when the `decoys` are exported, then they appear.
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So far rawDiag supports:
- iRT (Biognosys)
- 6 x 5 LC-MS/MS Peptide Ref. Mix (Promega)
- MSQC1 (Sigma)
Are there other peptide sets that could make sense?
**PROCAL**
Zolg, D. P., Wilhelm, …
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Currently this code works for peptides in 12 -24 AA range. it appears this in enforced for the percentile calculation. Would removing this limitation still allow for the log odd calcualtions?
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In the human analysis, I tried to cluster peptides based on characteristics (aliphatic index, length, etc.). While things like PCA explain a lot of the variance, the peptides all form a big blob no ma…