Nesvilab/MSFragger

Issues

• Missing 'Assigned Modifications' for N-terminal mods in detailed mass-offset search

  #328 opened 3 months ago by tjlundgren
  4

• Add nativeID output in mzIdentML/pepXML[/mzML/PIN]

  #324 opened 6 months ago by chambm
  9

• 4.1 writing _uncalibrated.mzML for RAW files

  #327 opened 5 months ago by chambm
  7

• Windows Java Configuration in Command Prompt

  #326 opened 6 months ago by kostrouc
  1

• Incorrect mzML tags broke MSFragger

  #323 opened 6 months ago by ClaSofMag
  14

• Index out-of-bound error when perform open search

  #317 opened 9 months ago by yonghanyu
  8

• MSBooster shows an error for non-specific HLA peptidomics - timsTOF data

  #321 opened 7 months ago by mshahbazy
  1

• Is it possible modify peptide level data before proceeding to protein quant?

  #316 opened 9 months ago by hboekweg
  1

• Low resolution MS database search

  #307 opened 9 months ago by Baopusr
  4

• Insufficient memory problem

  #313 opened 9 months ago by ShinjaChakraborty
  1

• Peptides with and without modficiation

  #315 opened 9 months ago by tanjagosnjak
  8

• Are DDA+ IDs of different ranks equal?

  #304 opened 10 months ago by candidaorelmex
  4

• Question about multiple PTMs on same residue

  #312 opened 10 months ago by JannikSchneider12
  1

• Question about PTM format

  #311 opened 10 months ago by JannikSchneider12
  1

• Does MSFragger allow two modifications on the same residue?

  #309 opened 10 months ago by HijaziHassan
  4

• Setting up variable modifications

  #308 opened 10 months ago by luizalmeida93
  2

• Error During pepxml Rewrite: Unable to Find Correct Mapping for Raw File Path

  #305 opened 10 months ago by Schwarzeneggerjune
  8

• nonspecific search

  #302 opened a year ago by Mohee66
  1

• Use a pre-digested database for close/open search

  #299 opened a year ago by yonghanyu
  4

• MS Fragger DDA+ parameter: What optimal setting for 'Report top N' for DDA+?

  #293 opened a year ago by prao123
  1

• Are processed MS/MS spectra decharged before database search carried out by MSFragger?

  #298 opened a year ago by HijaziHassan
  1

• Question: Extraction of scannumber

  #294 opened a year ago by JannikSchneider12
  2

• Cannot perform open search with precursor tolerance lower than -230 Da

  #290 opened a year ago by jossmi
  3

• FragPipe (v20.0) error following updates

  #291 opened a year ago by hcadre
  2

• .wiff convert to .mzML but non-centroid scans

  #287 opened a year ago by Ruby0416W
  1

• another stand-alone version

  #288 opened a year ago by hxxhust163
  2

• Extended Processing Time for MSFragger-PD Open Search

  #275 opened a year ago by jafarilab
  9

• TIMSTOF DDA TypeError: list indices must be integers or slices, not NoneType

  #285 opened a year ago by Wolfy0111
  3

• Coverage results missing

  #284 opened a year ago by Xindong-Sun
  2

• Program stopping with 1 Remaining Task

  #283 opened a year ago by kgraham96
  1

• B -Z amino acid fixed modifications

  #282 opened a year ago by DesAmsh
  3

• MS-Fragger dia for timsTOF diaPASEF

  #281 opened a year ago by rnirujogi
  2

• Java-related error of MSFragger 3.8 and FragPipe20.0

  #278 opened a year ago by jjnbdal
  1

• SpectralSim value

  #280 opened a year ago by patrick-willems
  2

• Various Workflow for DIA data

  #279 opened a year ago by TeckYewLow
  1

• Differences in quans & identified peptides with MSFragger in PD-node vs FragPipe

  #274 opened a year ago by FriedLabJHU
  14

• EasyPQP convert error

  #276 opened a year ago by gcrynen
  2

• FragPipe not working

  #272 opened a year ago by pankajdwid
  1

• Problem with MSFragger: java.lang.OutOfMemoryError: Java heap space

  #270 opened 2 years ago by yfeiiiii
  1

• Problem with MSFragger: java.lang.OutOfMemoryError: Java heap space

  #269 opened 2 years ago by yfeiiiii
  1

• Error in the use of DIA-Umpire for non-specific search and library free DIA analysis of HLA peptidomes

  #268 opened 2 years ago by shahbazymoh
  8

• Labile Search with Variable Modification

  #265 opened 2 years ago by xLinkKnight
  1

• Experimental RT and predicted RT data

  #266 opened 2 years ago by blucherxeus
  3

• Write the output to a new folder

  #267 opened 2 years ago by qussai96
  3

• DIA calibrate_mass = 1 error

  #263 opened 2 years ago by charlin90
  1

• Issue running fragPipe just installed (LFQ)

  #261 opened 2 years ago by BioMassSpec
  3

• Can MsFragger process samples in separate instances?

  #260 opened 2 years ago by charlin90
  3

• The delat mass of the modification is not consistent with the setting in the spectrum library

  #259 opened 2 years ago by atesora
  3

• Problem when running MSFragger on Mac

  #258 opened 2 years ago by nttvy
  1

• MSFragger fails on Thermo Ascend files

  #256 opened 2 years ago by im281
  2