Towards Guidelines for DIA Reporting Criteria
Data Independent Acquisition Interest Group
Presiders: Mike MacCoss, Michael Ford
Monday, June 2, 2025, 5:45 - 7:00pm in Ballroom IV
The guidelines for reporting mass spectrometry proteomics data were outlined over twenty years ago and have provided a solid calibrator for the field since that time. DIA specific guidelines were suggested in 2019. It is our thought that an update to these guidelines may be necessary to include properties unique to evolving DIA workflows. The purpose of this workshop is to provide a forum for the discussion of DIA reporting guidelines. In an informal but structured setting of an ASMS workshop the community can engage in an open discussion about how the criteria may look and be applied. It is our intention to engage several experts in the field before the meeting to 1) establish a highly qualified list of speakers and 2) outline a set of goals/discussion points to ensure a focused conversation.
Agenda:
- Mike MacCoss and John Yates: A 5 min opener on the need to come up with a common way of assessing FDR control. Bigger lists using different criteria 1) complicates tool comparisons and 2) can reduce quantitative sensitivity.
- Bo Wen: 10 min on recommendations for assessing reported FDR. For reference see Wen et al, Biorxiv 2025
- 10 min each for Alexey Nesvizhskii, Martin Frejno, and Oliver Bernhardt to discuss how they control FDR in their tools. Use the data as a possible example?
- With reference to this publication, we have secured raw files and a database for the differential analysis of 2 IP samples.
- Please share your results with everyone ahead of time and we will make a summary slide of the findings as 1) how many proteins/peptides are detectable at a 1% FDR and 2) how many proteins are enriched in the IP (either C22 or A31) versus the negative control (mCherry).
- There is also a fasta file that contains just the viral proteins and another that contains the viral proteins with the uniprot canonical protein sequences.