java.util.NoSuchElementException during Glycan Assignment in PTMShepherd (v23.0)

[cyH2001]

Subject: Bug Report: java.util.NoSuchElementException during Glycan Assignment in PTMShepherd (v23.0)
Description
I am reporting a fatal error encountered while running O-glycan assignment with a custom glycan database (861 entries) using FragPipe v23.0. The process terminates with a java.util.NoSuchElementException during the pairwiseCompareYstatic step.

System Environment

FragPipe Version: 23.0
Workflow: glyco-O-HCD.workflow
Module: PTMShepherd (Glyco Analysis)
Data Type: timsTOF HT DDA (dataset: timsTOF_HT_DDA_X0064260102...)
Key Parameters & Configuration

Glycan FDR: 3.0% / 5.0%
Mass Error: 30.0 ppm (also tested 50.0 ppm)
Isotope Errors: [-1, 0, 1, 2, 3]
Threads: Tested both multi-threaded and single-threaded (1). Both failed with the same error.
Error Log Highlights

java.util.concurrent.ExecutionException: java.util.NoSuchElementException
at java.base/java.util.concurrent.FutureTask.report(Unknown Source)
at edu.umich.andykong.ptmshepherd.glyco.GlycoAnalysis.glycoPSMs(GlycoAnalysis.java:128)
at edu.umich.andykong.ptmshepherd.PTMShepherd.runGlycanAssignment(PTMShepherd.java:571)
Caused by: java.util.NoSuchElementException
at java.base/java.util.TreeMap$PrivateEntryIterator.nextEntry(Unknown Source)
at java.base/java.util.TreeMap$ValueIterator.next(Unknown Source)
at edu.umich.andykong.ptmshepherd.glyco.GlycoAnalysis.pairwiseCompareYstatic(GlycoAnalysis.java:1261)
at edu.umich.andykong.ptmshepherd.glyco.GlycoAnalysis.pairwiseCompareStatic(GlycoAnalysis.java:1210)
java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
Fatal error: Error in parallel processing glyco PSMs
Process 'PTMShepherd' finished, exit code: 1
Process returned non-zero exit code, stopping
Troubleshooting & Observations
I attempted to modify the ptmshepherd.cap_y_ions parameter to narrow down the cause:

Modification A: Set ptmshepherd.cap_y_ions=0,203.07937.
Result: Still failed with java.util.NoSuchElementException. This suggests the iterator is failing even with standard Y-ion masses when using this specific custom database.
Modification B: Set ptmshepherd.cap_y_ions=0.
Result: The process "hangs." The GUI status shows "Finished," but the "RUN" button remains greyed out and only "STOP" is clickable. No output files are generated, and the log stops advancing. It seems the logic enters an infinite loop or an unhandled empty state.
Other attempts: Changing PPM to 50 and reducing/expanding isotope error ranges did not bypass the error.
Expected Behavior
The glycan assignment should either complete based on the provided Y-ion list or provide a clear error message if the Y-ion list is incompatible with the glycan database.

Requested Action
It seems there is a robustness issue in GlycoAnalysis.java when handling certain Y-ion configurations or custom glycan entries, specifically where a TreeMap iterator (likely for scoring Y-ions) is called without a safety check for empty elements. Any advice on a workaround or a fix for this would be much appreciated.

log_2026-03-10_11-43-46.txt

[dpolasky]

Hi,

It looks like the cause of the issue the NeuAc(1) and NeuGc(1) glycans in the database - we do not expect these to form any Y ions and this case is not handled in the code. We will implement a fix to allow these glycans to be searched, but in the meantime, you should be able to complete the search with the current version by removing these two glycans from the glycan database.

Best,
Dan

[cyH2001]

Hi Dan,

Thanks for the reply. I excluded both NeuGc(1) and NeuAc(1) from the glycan database, but the error still appears. Please see the attached log. I would appreciate your support.

Best,
cyH2001

log_2026-03-11_06-22-30.txt

[dpolasky]

Hi cyH2001,

I'm able to run successfully with your updated database (without NeuAc(1) or NeuGc(1)) with the current Fragpipe release version (24.0). Have you edited the glycan_residues or glycan_mods definitions at all? If so, that may be the issue and reverting those changes to defaults could resolve it. If not, can you try upgrading to the latest Fragpipe and running again?

Best,
Dan