Systematic characterization of site-specific proline hydroxylation using hydrophilic interaction chromatography and mass spectrometry

Reviewer #1 (Public review):

Summary:

The manuscript by Hao Jiang et al described a systematic approach to identify proline hydroxylation proteins. The authors implemented a proteomic strategy with HILIC-chromatographic separation and reported an identification of 4993 sites from HEK293 cells (4 replicates) and 3247 sites from RCC4 sites (3 replicates) with 1412 sites overlapping between the two cell lines. From the analysis, the authors identified 225 sites and 184 sites respectively from 293 and RCC4 cells with HyPro diagnostic ion. The identifications were validated by analyzing a few synthetic peptides, with a specific focus on Repo-man (CDCA2) through comparing MS/MS spectra, retention time, and diagnostic ions. With SILAC analysis and recombinant enzyme assay, the study showed that Repo-man HyPro604 is a target of the PHD1 enzyme.

Strengths:

The study involved extensive LC-MS analysis and was carefully implemented. The identification of over 4000 confident proline hydroxylation sites would be a valuable resource for the community. The characterization of Repo-man proline hydroxylation is a novel finding.

Weaknesses:

However, as a study mainly focused on methodology, the findings from the experimental data did not convincingly demonstrate the sensitivity and specificity of the workflow for site-specific identification of proline hydroxylation in global studies.

Major concerns:

(1) The study applied HILIC-based chromatographic separation with a goal of enriching and separating hydroxyproline-containing peptides. However, as the authors mentioned, such an approach is not specific to proline hydroxylation. In addition, many other chromatography techniques can achieve deep proteome fractionation such as high pH reverse phase fractionation, strong-cation exchange etc. There was no data in this study to demonstrate that the strategy offered improved coverage of proline hydroxylation proteins, as the identifications of the HyPro sites could be achieved through deep fractionation and a highly sensitive LCMS setup. The data of Figure 2A and S1A were somewhat confusing without a clear explanation of the heat map representations.

(2) The study reported that the HyPro immonium ion is a diagnostic ion for HyPro identification. However, the data showed that only around 5% of the identifications had such a diagnostic ion. In comparison, acetyllysine immonium ion was previously reported to be a useful marker for acetyllysine peptides (PMID: 18338905), and the strategy offered a sensitivity of 70% with a specificity of 98%. In this study, the sensitivity of HyPro immonium ion was quite low. The authors also clearly demonstrated that the presence of immonium ion varied significantly due to MS settings, peptide sequence, and abundance. With further complications from L/I immonium ions, it became very challenging to implement this strategy in a global LC-MS analysis to either validate or invalidate HyPro identifications.

(3) The study aimed to apply the HILIC-based proteomics workflow to identify HyPro proteins regulated by the PHD enzyme. However, the quantification strategy was not rigorous. The study just considered the HyPro proteins not identified by FG-4592 treatment as potential PHD targeted proteins. There are a few issues. First, such an analysis was not quantitative without reproducibility or statistical analysis. Second, it did not take into consideration that data-dependent LC-MS analysis was not comprehensive and some peptide ions may not be identified due to background interferences. Lastly, FG-4592 treatment for 24 hrs could lead to wide changes in gene expressions and protein abundances. Therefore, it is not informative to draw conclusions based on the data for bioinformatic analysis.

(4) The authors performed an in vitro PHD1 enzyme assay to validate that Repo-man can be hydroxylated by PHD1. However, Figure 9 did not show quantitatively PHD1-induced increase in Repo-man HyPro abundance and it is difficult to assess its reaction efficiency to compare with HIF1a HyPro.

Reviewer #2 (Public review):

Summary:

In this manuscript, Jiang et al. developed a robust workflow for identifying proline hydroxylation sites in proteins. They identified proline hydroxylation sites in HEK293 and RCC4 cells, respectively. The authors found that the more hydrophilic HILIC fractions were enriched in peptides containing hydroxylated proline residues. These peptides showed differences in charge and mass distribution compared to unmodified or oxidized peptides. The intensity of the diagnostic hydroxyproline iminium ion depended on parameters including MS collision energy, parent peptide concentration, and the sequence of amino acids adjacent to the modified proline residue. Additionally, they demonstrate that a combination of retention time in LC and optimized MS parameter settings reliably identifies proline hydroxylation sites in peptides, even when multiple proline residues are present

Strengths:

Overall, the manuscript presents an advanced, standardized protocol for identifying proline hydroxylation. The experiments were well designed, and the developed protocol is straightforward, which may help resolve confusion in the field.

Weaknesses:

(1) The authors should provide a summary of the standard protocol for identifying proline hydroxylation sites in proteins that can easily be followed by others.

(2) Cockman et al. proposed that HIF-α is the only physiologically relevant target for PHDs. Their approach is considered the gold standard for identifying PHD targets. Therefore, the authors should discuss the major progress they made in this manuscript that challenges Cockman's conclusion.

Reviewer #3 (Public review):

Summary:

The authors present a new method for detecting and identifying proline hydroxylation sites within the proteome. This tool utilizes traditional LC-MS technology with optimized parameters, combined with HILIC-based separation techniques. The authors show that they pick up known hydroxy-proline sites and also validate a new site discovered through their pipeline.

Strengths:

The manuscript utilizes state-of-the-art mass spectrometric techniques with optimized collision parameters to ensure proper detection of the immonium ions, which is an advance compared to other similar approaches before. The use of synthetic control peptides on the HILIC separation step clearly demonstrates the ability of the method to reliably distinguish hydroxy-proline from oxidized methionine - containing peptides. Using this method, they identify a site on CDCA2, which they go on to validate in vitro and also study its role in regulation of mitotic progression in an associated manuscript.

Weaknesses:

Despite the authors' claim about the specificity of this method in picking up the intended peptides, there is a good amount of potential false positives that also happen to get picked (owing to the limitations of MS-based readout), and the authors' criteria for downstream filtering of such peptides require further clarification. In the same vein, greater and more diverse cell-based validation approach will be helpful to substantiate the claims regarding enrichment of peptides in the described pathway analyses.

Author response:

Reviewer #1 (Recommendations for the authors):

We appreciate the reviewer recognising that our study has been carefully performed and provides a valuable resource for the community. The characterization of Repo-man proline hydroxylation is also recognised as a novel finding.

With respect to Concerns raised by reviewer 1:

(1) The study applied HILIC-based chromatographic separation with a goal of enriching and separating hydroxyproline-containing peptides. However, as the authors mentioned, such an approach is not specific to proline hydroxylation. In addition, many other chromatography techniques can achieve deep proteome fractionation such as high pH reverse phase fractionation, strong-cation exchange etc. There was no data in this study to demonstrate that the strategy offered improved coverage of proline hydroxylation proteins, as the identifications of the HyPro sites could be achieved through deep fractionation and a highly sensitive LCMS setup. The data of Figure 2A and S1A were somewhat confusing without a clear explanation of the heat map representations.

We do not agree that the apparent concern raised here, i.e., that the method we present is not 100% specific for enriching only hydroxylated peptides, is a serious issue. We show specifically that our method indeed enriches samples for hydroxylated peptides, thereby increasing the chances of identifying proline hydroxylated peptides in a cell extract. We never claimed that it was mono-specific for enrichment of hydroxylated peptides. Further, we note that almost no chromatographic method we know of, including those commonly used to enrich for different types of post translationally-modified peptides (including phospho-peptides) is completely mono-specific for a single type of modified peptide. The reviewer comments that it could have been possible to use alternative methods to identify proline-hydroxylated peptides. This may be true, but we know of no published examples, or previous studies, where this has been demonstrated experimentally on a scale comparable to that we show here. Of course there is always more than one way to approach technical challenges and it may be that future methods will be demonstrated that achieve equivalent, or even superior, results with respect to the detection of proline hydroxylated peptides. To the best of our knowledge, however, our current study provides a robust methodology that goes well beyond any previously published analysis of proline hydroxylation.

(2) The study reported that the HyPro immonium ion is a diagnostic ion for HyPro identification. However, the data showed that only around 5% of the identifications had such a diagnostic ion. In comparison, acetyllysine immonium ion was previously reported to be a useful marker for acetyllysine peptides (PMID: 18338905), and the strategy offered a sensitivity of 70% with a specificity of 98%. In this study, the sensitivity of HyPro immonium ion was quite low. The authors also clearly demonstrated that the presence of immonium ion varied significantly due to MS settings, peptide sequence, and abundance. With further complications from L/I immonium ions, it became very challenging to implement this strategy in a global LC-MS analysis to either validate or invalidate HyPro identifications.

We feel that the reviewer’s initial comment is potentially misleading - it implies that we were proposing here that the 'HyPro immonium ion is a diagnostic ion for HyPro identification’. In contrast, this concept was already widely held in the field before we started this project. Indeed, the fact that the diagnostic HyPro immonium ion is often difficult to detect, has been used as one of the arguments by other researchers to support the view that HIF-α is the only physiologically relevant target for PHD enzymes, a controversy referenced explicitly by Reviewer 2 below. What we actually show here are novel data that help to explain why the diagnostic HyPro immonium ion is often difficult to detect, when standard approaches and technical parameters for MS analysis are used. We beleive that this observation, along with other data we present, is a useful contribution to the field that can help to resolve the previous controversies concerning the true prevalence and biological roles of PHD-catalysed proline hydroxylation on protein targets.

(3) The study aimed to apply the HILIC-based proteomics workflow to identify HyPro proteins regulated by the PHD enzyme. However, the quantification strategy was not rigorous. The study just considered the HyPro proteins not identified by FG-4592 treatment as potential PHD targeted proteins. There are a few issues. First, such an analysis was not quantitative without reproducibility or statistical analysis. Second, it did not take into consideration that data-dependent LC-MS analysis was not comprehensive and some peptide ions may not be identified due to background interferences. Lastly, FG-4592 treatment for 24 hrs could lead to wide changes in gene expressions and protein abundances. Therefore, it is not informative to draw conclusions based on the data for bioinformatic analysis.

We agree that this study is not quantifying or addressing the stoichiometry of proline hydroxylation across the very large number of new PHD target sites we identify. That was not claimed and was not the objective of our study. Nonetheless, we feel the comments of the referee do not adequately take into account the SILAC data we included (cf Figure 8) or the full range of experimental data presented in this study. We would further refer the reviewer also to the data presented in the companion paper by Druker et al., which we cross-referenced extensively in our study and have also made available previously on biorxiv.

(4) The authors performed an in vitro PHD1 enzyme assay to validate that Repo-man can be hydroxylated by PHD1. However, Figure 9 did not show quantitatively PHD1-induced increase in Repo-man HyPro abundance and it is difficult to assess its reaction efficiency to compare with HIF1a HyPro.

Here again we refer to the recent controversy referenced explicitly by Reviewer 2 below, concerning the view expressed by some researchers that only HIF-α is a physiological substrate for PHD enzymes in cells. We were challenged to show that any of the novel protein targets of PHDs we identified were indeed hydroxylated by PHD enzymes in vitro and that is what we demonstrated in Figure 9. This was not an experiment performed to quantify stoichiometry and indeed, it is not possible to draw any firm conclusions about efficiency or stiochiometry in vitro when using catalytic PHD subunits alone, given that we do not yet know whether PHDs may show different properties in cells, dependent on interactions with other factors and/or modifications.

Reviewer #2 (Recommendations for the authors):

We appreciate the reviewer’s comments that our manuscript presents an advanced, standardized protocol for identifying proline hydroxylation, with well designed experiments, which may help resolve confusion in the field.

With respect to Concerns raised by reviewer 2:

(1) The authors should provide a summary of the standard protocol for identifying proline hydroxylation sites in proteins that can easily be followed by others.

We agree and plan to provide a clearly described, step by step guide to assist other researchers who wish to employ our methods for proline hydroxylation analysis in their own studies.

(2) Cockman et al. proposed that HIF-α is the only physiologically relevant target for PHDs. Their approach is considered the gold standard for identifying PHD targets. Therefore, the authors should discuss the major progress they made in this manuscript that challenges Cockman's conclusion.

We agree that our study provides valuable information germane to the recent controversy in the field and the views published by Cockman et al., to the effect that HIF-α is the only physiologically relevant target for PHDs. We will carefully review our statements when preparing a suitably revised version of record with the aim of providing a balanced and objective discussion of this issue.

Reviewer #3 (Recommendations for the authors):

We appreciate the reviewer’s comments that our study employs state-of-the-art mass spectrometric techniques with optimized collision parameters to ensure proper detection of the immonium ions, along with their recognition that our study is, 'an advance compared to other similar approaches before.’ We also appreciate their reference to our companion study by Druker et al, in which we characterise the mechanism and biological role in regulation of mitotic progression of the hydroxylation of P604 in the target protein RepoMan (CDCA2), that is identified in this study.

With respect to the Concern raised by reviewer 3:

Despite the authors' claim about the specificity of this method in picking up the intended peptides, there is a good amount of potential false positives that also happen to get picked (owing to the limitations of MS-based readout), and the authors' criteria for downstream filtering of such peptides require further clarification. In the same vein, greater and more diverse cell-based validation approach will be helpful to substantiate the claims regarding enrichment of peptides in the described pathway analyses..

We agree that this study, which has a focus on methodology and technical approaches for detecting sites of PHD- catalysed proline hydroxylation, cannot exhaustively validate the biological significance of all of the putative sites and targets identified. As the reviewer notes, we have performed a detailed functional characterisation of one such novel PHD-catalyed proline hydroxylation site, i.e. P604 in the protein RepoMan (CDCA2). This functional analysis is presented in the companion paper by Druker et al., which has also been reviewed by eLife and placed on biorxiv (doi: https://doi.org/10.1101/2025.05.06.652400). We hope that publication of our identification of many new putative PHD target sites will encourage other researchers to pursue characterisation of their functional reoles in different biological mechanisms and have tried here to provide some degree of guidance to focus attention on the identification of those sites for which we currently have highest confidence.