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Thanks for writing and maintaining the software. Our lab is using it to extract MS3 reporter ion intensities from peptide-spectrum matches identified by search software that does not support TMT-MS3 …
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As calibration is further improved and tested (especially for topdown data), if it was part of mzlib then these improvements could be used in proteoformsuite
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Hi,
I did some more testing and wanted to investigate some AlphaPept vs MaxQuant results in AlphaViz.
Here I noticed that the intensity values for MS2 fragments are different. More specifically, the…
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@percolator would be great to put in this issue a set of papers that contains algorithms we need to read for Consensus Spectrum creation. We can put some pseudo-code about the existing algorithms.
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This is rather a feature request than an issue. It would be nice if the PSM table could be string-queried-filtered (not just sorted) by ProteinID, Entry Name and protein Description. This feature wou…
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There are some functions that I would like to use in my everyday work and they are actually implemented, but hidden. I would like to ask you to expose them. The ones I would like straight away are 2…
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Hello,
trying to analyze samples that have been a) acquired with a 120min LC gradient and b) acquired with a 60min LC gradient.
The spectra from a) work well with msgf+. However, the spectra from b)…
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I am attempting to convert mztab peptide identification from casanovo to .blib format but have been unsuccessful using BlibBuild. The first error I recieved was:
```
(base) kostrouchov@myip:~$ ./B…
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It was already decided to allow multiple representations (txt, json, csv, hdf...) of the new spectral library format, based on a common framework (required (meta)data, controlled vocabulary...). In th…
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Dear Vadim,
we are trying to compare different workflows of DIA-NN for our data sets. While the 'baseline' would be including a fasta file and the DL-based prediction of spectra and retention times…