Nesvilab/FragPipe

Issues

• Fragpipe crashes with .raw files on linux system

  #1957 opened 3 months ago by apsteinberg
  10

• WWA workflow - MSFragger: .pin is empty. Will not process this file. (SCIEX 7600)

  #1956 opened 3 months ago by rtool1
  5

• Adding decoys and contaminants from the commandline?

  #1955 opened 3 months ago by apsteinberg
  5

• Improve the GUI to show some progress when installing Python packages

  #1941 opened 3 months ago by fcyu
  1

• TMT-Integrator doesn't allow for negative mass PTM's

  #1954 opened 4 months ago by ethangilmore
  4

• Process 'Percolator' finished, exit code: -1073741819 in Non-specific HLA DIA workflow

  #1949 opened 4 months ago by marthanik
  2

• TMT18 workflow for immunopeptidomics

  #1948 opened 4 months ago by NikolaMonteverde
  2

• How MSFRagger differentiate between DIA/DDA files?

  #1943 opened 4 months ago by yonist
  3

• Fragpipe decoys

  #1947 opened 4 months ago by ds2268
  1

• convert wiff to mzml

  #1952 opened 4 months ago by Kim03143
  1

• Unnormalized Data

  #1953 opened 4 months ago by aDenos24
  4

• I and L still occasionally mixed up

  #1919 opened 4 months ago by hollenstein
  10

• crashed with more LFQ files

  #1946 opened 4 months ago by zoe1985
  2

• IonQuant: java.lang.NullPointerException

  #1945 opened 4 months ago by kenlzh1996
  3

• Narraw (regular) search is working, but open search is not?

  #1921 opened 4 months ago by Ming339-uw
  3

• Group FDR control

  #1922 opened 4 months ago by JWJW1
  13

• Labeling quantification on phosphopeptides using DDA

  #1925 opened 4 months ago by GNMiller0114
  5

• nocleavage enzyme cut but error

  #1927 opened 4 months ago by ABChh26
  1

• Can't repeat the results of the previous search. Error with cache?

  #1929 opened 4 months ago by huongtran182
  5

• No combind_protein file

  #1932 opened 4 months ago by MariaStensland
  1

• Nonspecific-peptidome

  #1931 opened 4 months ago by nishimuy87
  3

• DIA data aquired from Astral is always failed

  #1934 opened 4 months ago by zoe1985
  2

• MS-Fragger DIA - DIAN-NN Quant failure to write MSstats output file

  #1935 opened 4 months ago by rnirujogi
  1

• Process 'PhilosopherFilter' finished, exit code: 2 Process returned non-zero exit code, stopping

  #1937 opened 4 months ago by talithar-star
  1

• Insufficient Memory Process 'MSFragger' finished, exit code: 1 Process returned non-zero exit code, stopping

  #1938 opened 4 months ago by talithar-star
  1

• database is locked. 'diaTracer' finished

  #1930 opened 4 months ago by Kokoushin
  1

• Don't bundle the Python zip files

  #1940 opened 4 months ago by fcyu
  5

• Question about protein grouping method of "combined_protein.tsv" + missing column in the file "combined_peptide.tsv"

  #1936 opened 4 months ago by RobAlbn
  8

• invalid spectrum file path

  #1933 opened 4 months ago by littlestar-416
  10

• Skyline stopped generating documents

  #1926 opened 4 months ago by ambgrav
  5

• Issue with SAINTexpress

  #1924 opened 4 months ago by larsonlarsoff
  7

• Peptides vs PSM files - Counts of identified peptides

  #1920 opened 4 months ago by diegomagassis
  3

• TMT 18

  #1915 opened 4 months ago by lukasz536
  2

• DDA nonspecific HLA search not enough memory

  #1918 opened 4 months ago by frankligy
  4

• Assinged modification were not displayed in psm.tsv under offset search

  #1917 opened 4 months ago by Bin-cc
  5

• About thermo raw files convert

  #1912 opened 4 months ago by Li5459000
  1

• User's badly formatted manifest file crashed FragPipe

  #1914 opened 4 months ago by frankligy
  8

• Fragpipe stopped at Philosopher

  #1916 opened 4 months ago by ibphuangchen
  2

• My file does not support scan modes

  #1913 opened 4 months ago by vagos3b
  1

• Generating spectral library by combining previous MSFragger results

  #1911 opened 4 months ago by owentsai
  4

• Process 'DIA-NN' finished, exit code: -1073741819

  #1910 opened 4 months ago by chad-hyer
  1

• Issue with DiaNN ERROR: C:\diann\src\diann.cpp: 19427: Cannot load spectral library

  #1908 opened 4 months ago by chad-hyer
  2

• Does not support scan modes: 9 (DIA) from ... file name

  #1907 opened 4 months ago by akyocum
  2

• Very long times in TimsTOF data + diaPASEF/diaTracer on semi-specific + variable modification searches (compared to Astral)

  #1905 opened 4 months ago by MiguelCos
  7

• No MBR feature and no quantification results

  #1901 opened 4 months ago by drstiltz
  8

• Settings influencing IonQuant intensity values

  #1900 opened 4 months ago by eldenrowland
  5

• Issue Loading FragPipe Results into Scaffold

  #1909 opened 4 months ago by mviolette95
  1

• DIA-spectlib-Quant output

  #1904 opened 4 months ago by Kim03143
  2

• add files

  #1903 opened 4 months ago by maohuanyang
  1

• TMT integrator - PTM on same AA, but different mass

  #1902 opened 4 months ago by jayieh
  6