MSGFPlus/msgfplus

Issues

• Got some negative values of MSGFScore in the output file when using ".mgf" file

  #132 opened 3 years ago by Sweetsour-crap
  1

• Some of the PSMs do have the corresponding scores in mzId

  #157 opened a month ago by ypriverol
  0

• All peptides were ranked "1" in output file

  #156 opened 3 months ago by JangHuang
  15

• Does MSGF+ support Bruker TDF files?

  #155 opened 6 months ago by hxxhust163
  2

• What is peptide isoform and how will it affect the MSGF+ search results?

  #154 opened 9 months ago by yonghanyu
  0

• How to validate the MSGF+ peptide searching data?

  #153 opened 9 months ago by MarcoPineapollo
  0

• number of peaks per spectrum

  #152 opened 9 months ago by ypriverol
  6

• MzIDToTsv error: Exception in thread "main" java.lang.IllegalStateException: Error initializing ID cache: No id attribute found for element null

  #128 opened 3 years ago by SophieSWChoi
  3

• Question about my parameter file

  #151 opened a year ago by JannikSchneider12
  5

• Generating decoy database + further processing

  #150 opened a year ago by JannikSchneider12
  5

• Problem with MzidToTsvConverter in WSL

  #149 opened a year ago by JannikSchneider12
  4

• Using trypsin vs no enzyme changes score on same PSM?

  #148 opened a year ago by glormph
  4

• Question about interpreting a low Qvalue but high(er) Evalue

  #147 opened a year ago by Hassan-1991
  0

• questions about Q-values in MSGF+

  #114 opened 4 years ago by Linkous-02
  4

• Protein FDR

  #146 opened 2 years ago by qzhang503
  2

• Supported OpenJDK version

  #145 opened 2 years ago by bernt-matthias
  2

• no valid spectra

  #144 opened 2 years ago by simonklaes
  8

• No peptides matched to decoy portion of the database

  #143 opened 2 years ago by LoayJabre
  0

• data format matters?

  #142 opened 2 years ago by hxxhust163
  4

• library error

  #141 opened 2 years ago by XuanangD
  0

• Java.lang.NegativeArraySizeException

  #140 opened 3 years ago by Luxxii
  2

• I occured a question when i try to convert .mzid to tsv

  #139 opened 3 years ago by fengwei-li
  0

• Error: Unable to access jarfile edu.ucsd.msjava.msdbsearch.BuildSA

  #138 opened 3 years ago by Luxxii
  1

• java.lang.ArrayIndexOutOfBoundsException: 0

  #110 opened 3 years ago by lydiayliu
  8

• mzid2tsv not working when previously was

  #136 opened 3 years ago by ryanpe13002
  5

• Unexpected low sensitivity for asp-n digested samples

  #137 opened 3 years ago by JB91451
  4

• Data independent acquitsition

  #135 opened 3 years ago by kmoad
  2

• Use already existing database help files

  #134 opened 3 years ago by Stortebecker
  1

• About Modification

  #133 opened 3 years ago by lbwfff
  4

• Combining identification results of fractions

  #130 opened 3 years ago by rkimoakbioinformatics
  2

• A question about the FDR and Q-Value of the MS-GF+ output

  #131 opened 3 years ago by Sweetsour-crap
  2

• MSGF+ parameter for mass spectra m/z bin width

  #125 opened 3 years ago by nattzy94
  1

• mods.txt for TMT6, TMT10, TMT11, iTRAQ4, iTRAQ8, and Label Free

  #129 opened 3 years ago by rkimoakbioinformatics
  2

• search progress stopped at 79.62% using MSGF+

  #127 opened 3 years ago by MAlinkous
  4

• How to get sample-level peptide identification data?

  #126 opened 3 years ago by rkimoakbioinformatics
  3

• Error when writing results: java.lang.ArrayIndexOutOfBoundsException: -8

  #124 opened 4 years ago by nattzy94
  6

• First time user, MANY Dynmods: MS-GF+ crashes

  #123 opened 4 years ago by r-cheologist
  5

• MSGF+ results without ion intensity of TMT 11 plex data

  #122 opened 4 years ago by sunqiangzai
  6

• Converting MS-GF+ mzid output to pepXML

  #117 opened 4 years ago by kevinkovalchik
  6

• java.lang.IndexOutOfBoundsException when opening mzML file

  #121 opened 4 years ago by BBBBunnyZ
  1

• Searching for the exact peptides in database provided

  #120 opened 4 years ago by lydiayliu
  6

• How can I use several spectrum files?

  #119 opened 4 years ago by Wang-kaifei
  3

• Questions about understanding the results

  #118 opened 4 years ago by Wang-kaifei
  2

• java.lang.NumberFormatException: For input string: "1-" over some data datasets

  #115 opened 4 years ago by mstambou
  24

• Is "ScoringParamGen" required?

  #116 opened 4 years ago by jian0104
  3

• Peptide is not linked back to ALL its source proteins in the MZID <PeptideEvidence> field

  #112 opened 4 years ago by realizor
  3

• Issue with spectrum indexing

  #113 opened 4 years ago by chrishuges
  2

• How to reduce MS-GF+ search time

  #108 opened 4 years ago by Jokendo-collab
  7

• How to exract spectral counts from pepXML

  #109 opened 4 years ago by Jokendo-collab
  0

• MSGF new enzyme help

  #107 opened 4 years ago by BaylorSci
  1