Discussions

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  Library generation using data from PeptideAtlas

  andrewlai started Nov 7, 2024 in General

  

  

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  Using full or smart profiling in cases where quant files are being aggregated from separate analyses

  Cajun-data asked Nov 6, 2024 in Q&A · Unanswered

  

  

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  Continued support for --learn-lib?

  enonimos asked Nov 5, 2024 in Q&A · Answered

  

  

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  Residue-specific proteomics (isoTOP-ABPP) with DIA-NN

  StephanHacker2 started Jun 14, 2024 in General

  

  

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  report.gg_matrix.tsv vs report.tsv

  AnirudhKashyap511 asked Oct 28, 2024 in Q&A · Unanswered

  

  

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  Spectrum libraries with modifications

  SamuelLozanoJuarez asked Oct 31, 2024 in Q&A · Unanswered

  

  

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  WARNING: it is strongly recommended to first generate an in silico-predicted library in a separate pipeline step and then use it to process the raw data, now without activating FASTA digest

  jeewan-rijal asked Oct 31, 2024 in Q&A · Answered

  

  

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  Precursor Counts

  abadgerw asked Oct 22, 2024 in Q&A · Answered

  

  

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  Program is not generating output

  Rodchalk asked Jul 29, 2022 in Q&A · Unanswered

  

  

  

  

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  How does DIA-NN calculate FDR?

  cframpas asked Oct 23, 2024 in Q&A · Unanswered

  

  

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  DIA-NN 1.9

  vdemichev started Jun 9, 2024 in General

  

  

  

  

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  DIA-NN 1.9.1 docker container

  MichelMoser started Sep 20, 2024 in General

  

  

  

  

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  Using RegEx within the 1.9.1 GUI

  dorvashmr started Oct 11, 2024 in General

  

  

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  Hydroxylation of proline as varmod

  GOzorun asked Oct 15, 2024 in Q&A · Unanswered

  

  

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  Request more than 5 var ptms

  BenoitBe asked Oct 16, 2024 in Q&A · Unanswered

  

  

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  Separate normalization

  GOzorun asked Oct 14, 2024 in Q&A · Unanswered

  

  

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  Quantification plexDIA SILAC DIA-NN 1.9

  alm3240 started Oct 10, 2024 in General

  

  

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  Analyze without Protease (peptidomic)

  BenoitBe asked Apr 25, 2022 in Q&A · Unanswered

  

  

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  Maximum size of FASTA file used

  SC0O8Y asked Sep 16, 2024 in Q&A · Unanswered

  

  

  

  

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  Steps to generate phosphosites_99.tsv file?

  sartoriius asked Aug 13, 2024 in Q&A · Unanswered

  

  

  

  

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  How to assess PTM localization confidence?

  Munchic asked Jul 5, 2022 in Q&A · Unanswered

  

  

  

  

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  Change disgestion site or trypsin

  BenoitBe asked Sep 25, 2024 in Q&A · Unanswered

  

  

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  Parquet format for spectral library storage

  enonimos started Sep 23, 2024 in General

  

  

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  Looking for suggestions on selecting software for downstream analysis.

  jeanchristophe13v asked Sep 23, 2024 in Q&A · Answered

  

  

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  How to Obtain Protein-Level Quantification from .parquet Files in DIA-NN 1.9.1 for Differential Analysis?

  YingtingPu asked Sep 17, 2024 in Q&A · Answered

  

  

  

  

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