MSGFPlus msgfplus issues

MSGFPlus / msgfplus

MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.

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issues

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All peptides were ranked "1" in output file

#156 JangHuang closed 1 month ago
15
Does MSGF+ support Bruker TDF files?

#155 hxxhust163 opened 4 months ago
2
What is peptide isoform and how will it affect the MSGF+ search results?

#154 yonghanyu opened 7 months ago
0
How to validate the MSGF+ peptide searching data?

#153 MarcoPineapollo opened 7 months ago
0
number of peaks per spectrum

#152 ypriverol closed 8 months ago
6
Question about my parameter file

#151 JannikSchneider12 opened 10 months ago
5
Generating decoy database + further processing

#150 JannikSchneider12 closed 10 months ago
5
Problem with MzidToTsvConverter in WSL

#149 JannikSchneider12 closed 10 months ago
4
Using trypsin vs no enzyme changes score on same PSM?

#148 glormph opened 1 year ago
4
Question about interpreting a low Qvalue but high(er) Evalue

#147 Hassan-1991 opened 1 year ago
0
Protein FDR

#146 qzhang503 closed 1 year ago
2
Supported OpenJDK version

#145 bernt-matthias opened 1 year ago
2
no valid spectra

#144 simonklaes opened 1 year ago
8
No peptides matched to decoy portion of the database

#143 LoayJabre closed 1 year ago
0
data format matters?

#142 hxxhust163 opened 2 years ago
4
library error

#141 XuanangD opened 2 years ago
0
Java.lang.NegativeArraySizeException

#140 Luxxii opened 2 years ago
2
I occured a question when i try to convert .mzid to tsv

#139 fengwei-li opened 2 years ago
0
Error: Unable to access jarfile edu.ucsd.msjava.msdbsearch.BuildSA

#138 Luxxii closed 2 years ago
1
Unexpected low sensitivity for asp-n digested samples

#137 JB91451 opened 2 years ago
4
mzid2tsv not working when previously was

#136 ryanpe13002 closed 2 years ago
5
Data independent acquitsition

#135 kmoad closed 2 years ago
2
Use already existing database help files

#134 Stortebecker opened 2 years ago
1
About Modification

#133 lbwfff opened 2 years ago
4
Got some negative values of MSGFScore in the output file when using ".mgf" file

#132 Sweetsour-crap opened 3 years ago
0
A question about the FDR and Q-Value of the MS-GF+ output

#131 Sweetsour-crap opened 3 years ago
2
Combining identification results of fractions

#130 rkimoakbioinformatics closed 3 years ago
2
mods.txt for TMT6, TMT10, TMT11, iTRAQ4, iTRAQ8, and Label Free

#129 rkimoakbioinformatics closed 3 years ago
2
MzIDToTsv error: Exception in thread "main" java.lang.IllegalStateException: Error initializing ID cache: No id attribute found for element null

#128 SophieSWChoi closed 3 years ago
3
search progress stopped at 79.62% using MSGF+

#127 MAlinkous closed 3 years ago
4
How to get sample-level peptide identification data?

#126 rkimoakbioinformatics closed 3 years ago
3
MSGF+ parameter for mass spectra m/z bin width

#125 nattzy94 closed 3 years ago
1
Error when writing results: java.lang.ArrayIndexOutOfBoundsException: -8

#124 nattzy94 closed 3 years ago
6
First time user, MANY Dynmods: MS-GF+ crashes

#123 r-cheologist opened 3 years ago
5
MSGF+ results without ion intensity of TMT 11 plex data

#122 sunqiangzai opened 3 years ago
6
java.lang.IndexOutOfBoundsException when opening mzML file

#121 BBBBunnyZ opened 3 years ago
1
Searching for the exact peptides in database provided

#120 lydiayliu closed 3 years ago
6
How can I use several spectrum files?

#119 Wang-kaifei opened 3 years ago
3
Questions about understanding the results

#118 Wang-kaifei closed 3 years ago
2
Converting MS-GF+ mzid output to pepXML

#117 kevinkovalchik closed 3 years ago
6
Is "ScoringParamGen" required?

#116 jian0104 closed 3 years ago
3
java.lang.NumberFormatException: For input string: "1-" over some data datasets

#115 mstambou opened 3 years ago
24
questions about Q-values in MSGF+

#114 Linkous-02 opened 3 years ago
4
Issue with spectrum indexing

#113 chrishuges closed 3 years ago
2
Peptide is not linked back to ALL its source proteins in the MZID <PeptideEvidence> field

#112 realizor closed 3 years ago
3
Bump junit from 4.11 to 4.13.1

#111 dependabot[bot] closed 4 years ago
0
java.lang.ArrayIndexOutOfBoundsException: 0

#110 lydiayliu closed 2 years ago
8
How to exract spectral counts from pepXML

#109 Jokendo-collab opened 4 years ago
0
How to reduce MS-GF+ search time

#108 Jokendo-collab opened 4 years ago
7
MSGF new enzyme help

#107 BaylorSci opened 4 years ago
1