ERROR: Failed to determine start of DIA cycle.

[nbacalzo507]

Hi,

I'm trying out AlphaDIA for the first time and I encountered this error message (see below). My files are from QExactive ran in staggered windows DIA acquisition. I'm wondering if the staggered window caused this error.

` File "alphadia\data\alpharaw.py", line 359, in init
self.process_alpharaw(**kwargs)
File "alphadia\data\alpharaw.py", line 277, in process_alpharaw
self.cycle, self.cycle_start, self.cycle_length = determine_dia_cycle(
^^^^^^^^^^^^^^^^^^^^
File "alphadia\data\alpharaw.py", line 194, in determine_dia_cycle
raise ValueError("Failed to determine start of DIA cycle.")
ValueError: Failed to determine start of DIA cycle.
0:13:46.788233 INFO: Traceback (most recent call last):
File "alphadia\data\alpharaw.py", line 268, in process_alpharaw
self.cycle, self.cycle_start, self.cycle_length = determine_dia_cycle(
^^^^^^^^^^^^^^^^^^^^
File "alphadia\data\alpharaw.py", line 194, in determine_dia_cycle
raise ValueError("Failed to determine start of DIA cycle.")
ValueError: Failed to determine start of DIA cycle.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "alphadia\cli.py", line 343, in run
plan.run()
File "alphadia\planning.py", line 363, in run
raise e
File "alphadia\planning.py", line 318, in run
workflow.load(dia_path, speclib)
File "alphadia\workflow\peptidecentric.py", line 122, in load
super().load(
File "alphadia\workflow\base.py", line 80, in load
self._dia_data = self._get_dia_data_object(dia_data_path)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "alphadia\workflow\base.py", line 201, in _get_dia_data_object
dia_data = alpharaw.Thermo(
^^^^^^^^^^^^^^^^
File "alphadia\data\alpharaw.py", line 359, in init
self.process_alpharaw(**kwargs)
File "alphadia\data\alpharaw.py", line 277, in process_alpharaw
self.cycle, self.cycle_start, self.cycle_length = determine_dia_cycle(
^^^^^^^^^^^^^^^^^^^^
File "alphadia\data\alpharaw.py", line 194, in determine_dia_cycle
raise ValueError("Failed to determine start of DIA cycle.")
ValueError: Failed to determine start of DIA cycle.

0:13:46.788233 �ERROR: Failed to determine start of DIA cycle.�`

[GeorgWa]

Hi, we haven't yet processed staggered window DIA data, yet this should be possible.
Can you share a raw file (some qc hela) with the acquisition method and upload it here: https://datashare.biochem.mpg.de/s/UFCrZBADX9JB22l

Best,
Georg

[tobiasko]

A suggestion: This article describes a benchmark data set for different DIA flavours on different instruments:

Van Puyvelde, B., Daled, S., Willems, S. et al. A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics. Sci Data 9, 126 (2022). https://doi.org/10.1038/s41597-022-01216-6

The DIA data from the qOrbitrap (AIF) is also staggered.

Best,
Tobi

[GeorgWa]

Hi, thanks for the ressource!
From the method table in the supplement I can't see any issue. We have processed a lot similar data. My guess is there is some overlap or there are repeated windows where the cycle determination fails.

Unfortunately Thermo raw files have no notion of a DIA cycle but knowing it greatly accelerates computation.

[nbacalzo507]

Unfortunately, I don't have HeLa injections with me. I'll double-check my acquisition method and play around with the demultiplexing too. thanks!