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Will you be able to extract the sequence window more flexibly? Could you get the predicted phosphosite in the middle of the window, so we can get the sequence of both the N and C terminus sides? I am …
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Very nice work! Have you compared VQGAN-LC with other quantizers like [FSQ](https://arxiv.org/abs/2309.15505) or [LFQ](https://arxiv.org/abs/2310.05737), which can also acheive high codebook utilizati…
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Can your script support LFQ phoshphoproteomic data generated from fragpipe. I have used two workflow in fragpipe, LFQ phospho and Labile_phospho and generated combined result for ptm site, peptides an…
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I used the following commands to run DIA-NN and got the above warning:
```
nice -19 /usr/diann/1.8.2_beta_8/linux/diann-1.8.1.8 --threads 32 --mass-acc 15 --mass-acc-ms1 15 --matrices --pg-level 1…
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Hi Phil,
I was experimenting with FSQ/LFQ for 3d-motion autoencoder and was wondering how to work through LFQ variety of options?
With FSQ its quite straight forward as it does not have any losses…
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**Describe the bug**
Hello,
I am currently using MaxQuant for data analysis and have encountered an issue after updating from version 2.0.3.0 to 2.5.2.0. Previously, the Peptides.txt file used to …
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Hi Fragpipe developers,
I'm trying to do a protein ID and LFQ of 12 samples using Fragpipe on the CLI, just like many times before. I ran into this issue in the mass calibration and parameter optim…
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### Description of the bug
```
ERROR ~ Error executing process > 'NFCORE_QUANTMS:QUANTMS:LFQ:PROTEOMICSLFQ (PXD002854-serum.sdrf_openms_design)'
Caused by:
Process `NFCORE_QUANTMS:QUANTMS:LFQ:…
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We tried to make paired analyses using the experimental_annotation column "replicate", but this setup
| condition | replicate |
|----------|:-------------:|
| A | 1 |
| A | 2 |
| A | 3 |
| B |…