iPRG-2023 Crosslinking MS Study Letter - Access, Analyze, Submit Results

Sep 2, 2026

This letter invites iPRG-2023 study participants to access provided datasets, complete crosslinking MS data analysis, and submit human-interpretable results. It explains that tutorials are available for the first half of the data to support participants with basic data-dependent acquisition MS knowledge, while guidance is not provided for the second half. The study aims to compare analytical techniques for crosslinked peptide identification, validation, and visualization, using common experimental crosslinking conditions (DSSO) across two protein-complex datasets. Submission is due by January 15, 2024.

LanguageEnglish

CategoryLetters

FormatDOCX

Pages4

Reading Time2 min

AccessFree to download

Study participation and deadlines

Study overview: crosslinking MS and analysis goals

Analysis approach and pipeline guidance

Instructions for datasets and required outputs

Deliverables and submission requirements

iPRG-2023 Proteome Informatics Research Group Study on Crosslinking MS Data Analysis Dear iPRG-2023 Study Participant, Thank you for your interest in this year's ABRF Proteome Informatics Research Group (iPRG) study. This letter provides the instructions needed to access the data files, complete your analysis, and submit your results. This the first iPRG study in which guided tutorials will be made available for analysis of the first half of the data, facilitating participation by novices to crosslinking MS data analysis. Guidance will not be provided for analysis of the second half of the data. Experienced participants are encouraged to use their own analysis pipeline for the entirety of the data, to provide greater diversity in the results collected. This will permit better comparison of analytical techniques for analysis of crosslinking MS data. The deadline for submission of your results is January 15, 2024 to qualify for inclusion in the study report that will be presented at the next ABRF Annual Meeting in Minneapolis, April, 2024. Study Overview Crosslinking MS is performed to infer interaction sites between proteins and structural restraints from individual proteins in purified or enriched protein complexes, or the full complement of proteins in a cellular lysate. For most experiments, proteins are chemically crosslinked, enzymatically digested, and analyzed by data-dependent acquisition on a high-performance mass spectrometer. Protein structure restraints and interactions are inferred by the identification of two distinct peptide sequences crosslinked in a tandem mass spectrum derived from a single precursor ion. Although crosslinked peptide analysis is fundamentally the same as typical data-dependent MS peptide analysis, processing pipelines for crosslinked peptide data often require specialized algorithms with parameters and constraints that differ from the more familiar ones employed for traditional protein identification/characterization. Coupled with the fact that crosslinked peptides are often sparsely observed in samples, validation and visualization of the data and results to produce confident and coherent conclusions is not trivial. The goal of this study is to gain information from the proteomics community about the different approaches for crosslinked peptide MS data analysis, showcasing the multitude of different pipelines and tools available, and providing guidance for improving the presentation of crosslinked MS results. In contrast to iPRG studies in the past, we are providing tutorials for analyzing the first half of the data in the study. These tutorials are designed such that any participant with basic knowledge of data-dependent acquisition MS data analysis can participate without any prior knowledge of crosslinked peptide mass spectrometry. With this approach, we hope to encourage participation by non-specialists and to better understand the common pitfalls users encounter when learning to perform crosslinked peptide analysis. Since we're not providing guidance for the analysis of the second half of the data, novice participants will be challenged to apply what they've learned and process a separate dataset on their own. Exploring pipelines in addition to the ones presented in the tutorials and obtained from the scientific literature and community are highly encouraged. Participants with prior experience in crosslinked peptide analysis are encouraged to forego the tutorials entirely and proceed with their preferred pipeline on the complete data set. Instructions Participants are asked to use one or more database search methods to identify crosslinked residues of protein complexes from data-dependent mass spectrometry data. Two datasets of different protein complexes are provided for which the participants must identify a) the proteins that are crosslinked to each other, b) the specific residues that are crosslinked, and c) the certainty or confidence (e.g., probabilities or q-values) of their conc

FAQs

What is the deadline to submit results for the iPRG-2023 study?

Results must be submitted no later than January 15, 2024 to qualify for inclusion in the study report presented at the next ABRF Annual Meeting in April 2024.

Does the letter provide tutorials for analyzing all of the data?

Tutorials are provided for the first half of the datasets. No guidance is provided for the second half, and participants are expected to process it using what they learned or their own pipeline.

What information must participants report when analyzing the datasets?

Participants must use database search methods to identify crosslinked residues and report (a) the crosslinked proteins, (b) the specific crosslinked residues, and (c) confidence measures such as probabilities or q-values.

Sep 2, 2026

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