Nesvilab / MSFragger

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

https://msfragger.nesvilab.org

Nesvilab/MSFragger Issues

Missing 'Assigned Modifications' for N-terminal mods in detailed mass-offset search
Updated 5 days ago4
Add nativeID output in mzIdentML/pepXML[/mzML/PIN]
Updated 8 days ago9
4.1 writing _uncalibrated.mzML for RAW files
Closed 2 months ago7
Windows Java Configuration in Command Prompt
Closed 2 months ago1
Incorrect mzML tags broke MSFragger
Closed 3 months ago14
Index out-of-bound error when perform open search
Closed 5 months ago8
MSBooster shows an error for non-specific HLA peptidomics - timsTOF data
Closed 4 months ago1
Is it possible modify peptide level data before proceeding to protein quant?
Closed 5 months ago1
Low resolution MS database search
Closed 6 months ago4
Insufficient memory problem
Closed 6 months ago1
Peptides with and without modficiation
Closed 6 months ago8
Are DDA+ IDs of different ranks equal?
Closed 7 months ago4
Question about multiple PTMs on same residue
Closed 6 months ago1
Question about PTM format
Closed 6 months ago1
Does MSFragger allow two modifications on the same residue?
Closed 6 months ago4
Setting up variable modifications
Closed 7 months ago2
Error During pepxml Rewrite: Unable to Find Correct Mapping for Raw File Path
Closed 7 months ago8
nonspecific search
Closed 8 months ago1
Use a pre-digested database for close/open search
Closed 8 months ago4
MS Fragger DDA+ parameter: What optimal setting for 'Report top N' for DDA+?
Closed 8 months ago1
Are processed MS/MS spectra decharged before database search carried out by MSFragger?
Closed 8 months ago1
Question: Extraction of scannumber
Closed 8 months ago2
Cannot perform open search with precursor tolerance lower than -230 Da
Closed 9 months ago3
FragPipe (v20.0) error following updates
Closed 9 months ago2
.wiff convert to .mzML but non-centroid scans
Closed 10 months ago1
another stand-alone version
Closed a year ago2
Extended Processing Time for MSFragger-PD Open Search
Closed a year ago9
TIMSTOF DDA TypeError: list indices must be integers or slices, not NoneType
Closed a year ago3
Coverage results missing
Closed a year ago2
Program stopping with 1 Remaining Task
Closed a year ago1
B -Z amino acid fixed modifications
Closed a year ago3
MS-Fragger dia for timsTOF diaPASEF
Closed a year ago2
Java-related error of MSFragger 3.8 and FragPipe20.0
Closed a year ago1
SpectralSim value
Closed a year ago2
Various Workflow for DIA data
Closed a year ago1
Differences in quans & identified peptides with MSFragger in PD-node vs FragPipe
Closed a year ago14
EasyPQP convert error
Closed a year ago2
FragPipe not working
Closed a year ago1
Problem with MSFragger: java.lang.OutOfMemoryError: Java heap space
Closed a year ago1
Problem with MSFragger: java.lang.OutOfMemoryError: Java heap space
Closed a year ago1
Error in the use of DIA-Umpire for non-specific search and library free DIA analysis of HLA peptidomes
Closed a year ago8
Labile Search with Variable Modification
Closed a year ago1
Experimental RT and predicted RT data
Closed a year ago3
Write the output to a new folder
Closed a year ago3
DIA calibrate_mass = 1 error
Closed a year ago1
Issue running fragPipe just installed (LFQ)
Closed a year ago3
Can MsFragger process samples in separate instances?
Closed a year ago3
The delat mass of the modification is not consistent with the setting in the spectrum library
Closed a year ago3
Problem when running MSFragger on Mac
Closed a year ago1
MSFragger fails on Thermo Ascend files
Closed 2 years ago2