xiaoxiang Huang

Fragments used in quantification

3

Hi Thanks for your work in DIA-NN, it really of high performance. I used DIANN by: diann-1.8.1 --dir /HYE124 --threads 32 --verbose 4 --out lib-base --lib lib.tsv --fasta human_yeast_ecoli_20140403_iRT_reverse.fasta --mass-acc...

values in the main output

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Hi Thanks for your work in DIA-NN. I used DIANN-1.8.1 to analyze the DIA files in library-based mode. The library contained 6 fragments for each precursor. Following is the cmd:...

Supported fragmentlosstype?

4

Hi Thanks for your work in Alphapeptdeep. I found a tsv_str your provided in the /nbdev_nbs/pipeline_api.ipynb containing 'noloss, H3PO4, 1(+H2+O)1(+H3+O4+P)' in the FragmentLossType column. I wonder whether peptdeep supports the...

checkpoint model

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hi Thanks for your work in developing Instanovo. I have installed it on my linux system following the installation instruction. But I encountered problems in using your software. Please help,...

how to calculate pr_matrix.tsv

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Hi Thanks for your work in DiaNN. I used Diann1.8.1 in linux system and have a few questions about '--qvalue' and '--matrix-qvalue' . With the same DIA data, spectral library...

specify number of fragments in quantification

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Hi Vadim Thanks for your work in DiaNN. I find that in the main out, the largest number of fragments used in quantification is 12. I mean the number of...

How is a precursor confidently identified?

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Hi Vadim Hope this finds you well. Thanks for your work in DiaNN. I get a library for DDA data. Based on the intensity, I get two libraries, one is...