In Silico Tools and Phosphoproteomic Software Exclusives

Round 1

Reviewer 1 Report

The article by Piby Paul et al. needs language improvement, Proof reading by a native English speaker is necessary to improve the text presentation. The manuscript requires an attractive title that reflects the content of the review. An entire section (section 2) entitled “Biocomputational tools for proteomics-A Snapshot” is dedicated for proteomics, but how this section is related to phosphoproteomics tools?  – the authors needs to explore it in the text. Section 3: the authors need to give subtitles of each tool related to phosphoproteomics and then explain the importance, applications, and required improvements.

Author Response

Response to reviewers comments

We greatly appreciate the Editor and the team of four reviewers for their extensive and prompt review. We have received valuable inputs and suggestions to our manuscript. Thankyou. We have now revised the manuscript as much as possible based on the suggestions, we have indicated the revisions in the text using track changes and also have addressed the queries point by point below. Thank you for your most valuable and constructive inputs.

Reviewer 1

The article by Piby Paul et al. needs language improvement, Proof reading by a native English speaker is necessary to improve the text presentation.

Ans. We have now revised the language and have now had the manuscript proof read by a native English speaker, the manuscript will now be devoid of any language errors.

The manuscript requires an attractive title that reflects the content of the review.

Ans. We have revised the title, thank you.

An entire section (section 2) entitled “Biocomputational tools for proteomics-A Snapshot” is dedicated for proteomics, but how this section is related to phosphoproteomics tools?  – the authors needs to explore it in the text.

Ans.  Yes we do understand your concern, since phosphoproteomics is a rather narrow field. We thought that we will start off giving a glimpse of the software tools available for proteomics which is the main stream field. Also in adding section 2 before section 3…. we intend the readers to have a comparison of how limited the tools for phosphoproteomics are compared to the tools on proteomics. This is why we felt that this section would be needed. Thank you for your kind understanding.

 Section 3: the authors need to give subtitles of each tool related to phosphoproteomics and then explain the importance, applications, and required improvements.

Ans. We have now given subtitles in the text and also have added a new table that gives a clear outlook of the message conveyed in the text. Thank you for your patience and time.

Reviewer 2 Report

Major Comment: Although the paper briefs on the tools in a clear fashion. It becomes imperative to include figures (block diagrams) similar to figure 1. Especially in section 2,3, The long paragraphs describing the tools one after the other makes it difficult for common reader to comprehend. It would be beneficial to the community if this is also presented as a table including features.  

Author Response

Reviewer 2

Major Comment: Although the paper briefs on the tools in a clear fashion. It becomes imperative to include figures (block diagrams) similar to figure 1. Especially in section 2,3, The long paragraphs describing the tools one after the other makes it difficult for common reader to comprehend. It would be beneficial to the community if this is also presented as a table including features.

Ans. Yes we agree that the texts are becoming hard for the readers to read and confusing. We have now aligned the text and also have added a new table which benefits the readers to have birds eye view on the tools, before reading the text. Thank you.

Reviewer 3 Report

        The review entitled “Bioinformatic reserves available for phosphoproteomics” has a clear message to the wide readership. The Authors are trying to encourage researchers to use all the numerous available bioinformatic tools with the aim to achieve outstanding goals in the field of phosphoproteomics. This message can be read in the Abstract, in the section 4 and in the Conclusions. The rest of the manuscript is quite hard to read mostly because of the uncountable names, abbreviations and hyperlinks to bioinformatic resources that are listed through it. I would like to suggest some improvements to the text aimed to increase the deliverance of the main message of this manuscript.

There is a lack of introductory section on the biochemistry of phosphorylation. The inclusion of a section that describes how, why and where proteins are phosphorylated will increase the number of readers largely. There is a lack of section on bioinformatic tools used to predict phosphorylation sites in proteins. Even though the data on confirmed phosphorylation sites are growing in the geometric progression, there are still numerous predicted sites in public data bases like UniProt. So, readers will be happy to read how reliable are those predictions and what are the distinguishing properties of Ser, Thr and Tyr residues that are usually phosphorylated. Also it is necessary to rearrange the text on numerous data bases and tools. Probably, a certain scheme of the description should be followed every time the Authors try to describe a group of methods. For example: 1) the purpose of usage of a group of bioinformatics tools; 2) the list of tools; 3) benefits of those tools; 4) limitations and disadvantages; 5) current achievements with a help of some of those tools; 6) future direction of their development.

Author Response

Reviewer 3

The review entitled “Bioinformatic reserves available for phosphoproteomics” has a clear message to the wide readership. The Authors are trying to encourage researchers to use all the numerous available bioinformatic tools with the aim to achieve outstanding goals in the field of phosphoproteomics. This message can be read in the Abstract, in the section 4 and in the Conclusions. The rest of the manuscript is quite hard to read mostly because of the uncountable names, abbreviations and hyperlinks to bioinformatic resources that are listed through it. I would like to suggest some improvements to the text aimed to increase the deliverance of the main message of this manuscript.

Ans. Thank you for your kind encouraging words and suggestions. We have now revised the manuscript to check on the aspects you have indicated and have also added a table as Table 1 that will help in directing the reader to have an understanding on the message in the text. Thankyou for your patience.

There is a lack of introductory section on the biochemistry of phosphorylation. The inclusion of a section that describes how, why and where proteins are phosphorylated will increase the number of readers largely.

Ans. Yes we agree, we have now added a short passage on the biochemistry of phosphorylation.

There is a lack of section on bioinformatic tools used to predict phosphorylation sites in proteins. Even though the data on confirmed phosphorylation sites are growing in the geometric progression, there are still numerous predicted sites in public data bases like UniProt. So, readers will be happy to read how reliable are those predictions and what are the distinguishing properties of Ser, Thr and Tyr residues that are usually phosphorylated.

Ans. We apologize sincerely, we had infact left out this section ….really sorry. We have now added a new passage section 3.3 on this topic. Thank you for guiding us.

Also it is necessary to rearrange the text on numerous data bases and tools. Probably, a certain scheme of the description should be followed every time the Authors try to describe a group of methods. For example: 1) the purpose of usage of a group of bioinformatics tools; 2) the list of tools; 3) benefits of those tools; 4) limitations and disadvantages; 5) current achievements with a help of some of those tools; 6) future direction of their development. 

Ans. We have rearranged the text and also have added a new table that kind of groups the tools based on their application, and orients the reader when they take a look at the text. Table 1 has been added in the revision. Thank you very much.

 

Reviewer 4 Report

The Manuscript “processes-630629” entitled: “Bioinformatic reserves available for phosphoproteomics” by Piby Paul, Manikandan Muthu, Yojitha Chilukuri, Sechul Chun is an interesting guide for proteomics and phosphoproteomic studies through the numerous available online tools. Unfortunately, this review reports a long list of bioinformatic tools and databases not completely or correctly describing what they do, not reporting information to connect the reader at the tool (In my opinion important in this review), often reporting misleading information regarding the use of the tools. For this reason, I suggest a thorough revision of the manuscript. Even if the manuscript is focalized on bioinformatic tools for phosphoproteomics, I suggest to better organize the “Biocomputational tools for proteomics-A Snapshot” section, perhaps introducing a table where are reported the tools or databases, subdivided per functions with the relative link, for instance starting from tools for protein or phospho-site identification, passing through the predictive tools, statistical tools and so on. In the section could be better explained the importance and the functions of these tools reporting at the table.

 

Major revision

Introducing Biocomputational tools for proteomics you made a long list of tools used in proteomics and not only, mixing together software with different functions in protein analysis. In order to better understand their functions, it could be better describing every type in a proper group in order to make the information more accessible to a researcher. Moreover, there are tools and software that are not working, perhaps expired? Please check every tool to be sure that all reported are working, in order to report really useful tools. In Biocomputational tools for proteomics section are also reported database not completely related to proteomics such as siRNAScanner, π-calculus and Stochastic Pi Machine (SPiM), PupaSuite, UTRscan and miRBase computational tools etc… Explain better why you report also these tools and why are important for proteomics. It is reported MODELLER 9v2 software was used to predict the 3-Dimensional structure of Cathepsin L Protein. Why only Cathepsin L? I suppose that could be better describe the generic functions of the tool that you are reporting. Together with every tool will be better report the corresponding link of access (for instance, in a table) in order to make usable that tool to the reader. You also report: “Magnetic bead based purification using a ClinProt system, using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) was used to successfully profile human tear proteins”. This method is not based on a bioinformatic tool but is a particular sample preparation and loading tool for MALDI ToF analysis. Page 6 line 209: skyline and MaxQuant are not software able to generating pathway networks and protein–protein interactions. Skyline is a freely-available and open source Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM), Data Independent Acquisition (DIA/SWATH) and DDA with MS1 quantitative methods and analyzing the resulting mass spectrometer data. While MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Both could be reported in the Biocomputational tools for proteomics section. GSEA (Gene Set Enrichment Analysis), is not only useful for inference of kinase activity from phosphoproteomics data. It could be applied to an entire set of gene expression data in order to obtain a huge number of information. In “Biocomputational tools for phosphoproteomics” paragraph are reported interesting software but could be better described relies on their functions, with a logic organization, as I suggested for the previous paragraph.

 

Minor revision

Please check typo errors. Page 6 line 229: you already reported PHOSIDA before in the paragraph.

 

Author Response

Reviewer 4

he Manuscript “processes-630629” entitled: “Bioinformatic reserves available for phosphoproteomics” by Piby Paul, Manikandan Muthu, Yojitha Chilukuri, Sechul Chun is an interesting guide for proteomics and phosphoproteomic studies through the numerous available online tools. Unfortunately, this review reports a long list of bioinformatic tools and databases not completely or correctly describing what they do, not reporting information to connect the reader at the tool (In my opinion important in this review), often reporting misleading information regarding the use of the tools. For this reason, I suggest a thorough revision of the manuscript. Even if the manuscript is focalized on bioinformatic tools for phosphoproteomics, I suggest to better organize the “Biocomputational tools for proteomics-A Snapshot” section, perhaps introducing a table where are reported the tools or databases, subdivided per functions with the relative link, for instance starting from tools for protein or phospho-site identification, passing through the predictive tools, statistical tools and so on. In the section could be better explained the importance and the functions of these tools reporting at the table.

Ans. We thankyou for your detailed review and revision opportunity. We have made changes whereever appropriate in the revision. Please find the specific responses below

Major revision

Introducing Biocomputational tools for proteomics you made a long list of tools used in proteomics and not only, mixing together software with different functions in protein analysis. In order to better understand their functions, it could be better describing every type in a proper group in order to make the information more accessible to a researcher. Moreover, there are tools and software that are not working, perhaps expired? Please check every tool to be sure that all reported are working, in order to report really useful tools.

Ans. Yes, we do see that this is a major concern, we have now added a table that will be used as a guideline for the readers to understand the text, this table has the tools categorized based on their function. This is table 1 in the revised version. We have also checked on the manuscript in terms of the tools as much as possible and updated it. Thank you.

 In Biocomputational tools for proteomics section are also reported database not completely related to proteomics such as siRNAScanner, π-calculus and Stochastic Pi Machine (SPiM), PupaSuite, UTRscan and miRBase computational tools etc… Explain better why you report also these tools and why are important for proteomics.

Ans. Yes, sorry about that, didn’t notice, we have removed these in the revision. Thank you.

 It is reported MODELLER 9v2 software was used to predict the 3-Dimensional structure of Cathepsin L Protein. Why only Cathepsin L? I suppose that could be better describe the generic functions of the tool that you are reporting. Together with every tool will be better report the corresponding link of access (for instance, in a table) in order to make usable that tool to the reader. You also report: “Magnetic bead based purification using a ClinProt system, using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) was used to successfully profile human tear proteins”. This method is not based on a bioinformatic tool but is a particular sample preparation and loading tool for MALDI ToF analysis. Page 6 line 209: skyline and MaxQuant are not software able to generating pathway networks and protein–protein interactions. Skyline is a freely-available and open source Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM), Data Independent Acquisition (DIA/SWATH) and DDA with MS1 quantitative methods and analyzing the resulting mass spectrometer data.

Ans. Very useful tips, your expertise has indeed guided us, we have changed all of the above in light of your suggestions. We have rewritten theSkyline and MaxQuant descriptions too. Thank you very much.

 While MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Both could be reported in the Biocomputational tools for proteomics section.

Ans. Yes it is as you have said they were basically proteomic tools, but both these (Max Quant and Skyline) have also been applied for phosphoproteomics and that’s why we have mentioned them in this section.

GSEA (Gene Set Enrichment Analysis), is not only useful for inference of kinase activity from phosphoproteomics data. It could be applied to an entire set of gene expression data in order to obtain a huge number of information.

Ans.  We have added this information too.

 In “Biocomputational tools for phosphoproteomics” paragraph are reported interesting software but could be better described relies on their functions, with a logic organization, as I suggested for the previous paragraph.

Ans. Yes organized now…also Table 1 introduced. Thankyou very much for your time and efforts, you have really shaped up the manuscript. Thank you for working with us on this manuscript.

Minor revision

Please check typo errors. Page 6 line 229: you already reported PHOSIDA before in the paragraph.

Ans. Yes you are right, checked and corrected now. Thankyou again.

 

 

Round 2

Reviewer 1 Report

The authors have improved the manuscript by revisions. However, some types have to be corrected. For example, the words genomics, epigenomics, lipidomics, glycomics, and transcriptomics do not need capital letters (lines 54-55). In other example, the word phosphoproteomics does not need capital letter (lines 62-63). Minor spell check required throughout  the manuscript.                                                                                                                                                                                                                                                                                                                                                                                                                                                                    

Author Response

Thankyou for your precious time and suggestions....we have now corrected the spellings and typos as you have suggested. Thank you

Reviewer 3 Report

In my opinion, revised version of the current review is better than the initial one.

Author Response

In my opinion, revised version of the current review is better than the initial one.

thank you....we have now revised the english language and style

Thank you

Reviewer 4 Report

The new version of the Manuscript “processes-630629” entitled: “In silico tools and phosphoproteomic software exclusives” by Piby Paul et al. is well elaborated and corrected. Each tool is in a proper paragraph in order to better understand its function. In my opinion the review is now ready to be published, paying attention to the minor revisions and to upload the missing table 1.

 

Minor revision

AC2Dgel tool is not in use. You can report SWISS 2DPAGE, as a 2Dgel database. Mascot is useful in protein identification by Peptide mass fingerprinting; PepMAPPER is not another Peptide mass fingerprinting tool. It is a web-based mapping tool developed for the purpose of epitope prediction and it is also useful in sequence-structure alignment for proteins because the core of these programs is an alignment-based algorithm Table 1 is not reported the in the manuscript. Please check typo errors along all the manuscript

The new version of the Manuscript “processes-630629” entitled: “In silico tools and phosphoproteomic software exclusives” by Piby Paul et al. is well elaborated and corrected. Each tool is in a proper paragraph in order to better understand its function. In my opinion the review is now ready to be published, paying attention to the minor revisions and to upload the missing table 1.

 

Minor revision

AC2Dgel tool is not in use. You can report SWISS 2DPAGE, as a 2Dgel database. Mascot is useful in protein identification by Peptide mass fingerprinting; PepMAPPER is not another Peptide mass fingerprinting tool. It is a web-based mapping tool developed for the purpose of epitope prediction and it is also useful in sequence-structure alignment for proteins because the core of these programs is an alignment-based algorithm Table 1 is not reported the in the manuscript. Please check typo errors along all the manuscript

Author Response

AC2Dgel tool is not in use. You can report SWISS 2DPAGE, as a 2Dgel database. Mascot is useful in protein identification by Peptide mass fingerprinting; PepMAPPER is not another Peptide mass fingerprinting tool. It is a web-based mapping tool developed for the purpose of epitope prediction and it is also useful in sequence-structure alignment for proteins because the core of these programs is an alignment-based algorithm Table 1 is not reported the in the manuscript. Please check typo errors along all the manuscript 

Thankyou dear reviewer for your highly valuable inputs and correcting us.....we are indebted. We have now revised as above and also have mentioned the Table....Thank you very much

Round 3

Reviewer 4 Report

This version of the manuscript is ready to be published