Submit to Molecules Review for Molecules Propose a Special Issue

Journal Browser

► Journal Browser

Advancements in Analytical Techniques for Proteomics

Special Issue Editors
Special Issue Information
Keywords
Published Papers

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Bioorganic Chemistry".

Deadline for manuscript submissions: closed (31 October 2021) | Viewed by 36208

Share This Special Issue

Special Issue Editors

Dr. Susy Piovesana

E-Mail Website
Guest Editor

Department of Chemistry, SAPIENZA Università di Roma, P.le A. Moro 5, 00185 Rome, Italy
Interests: analytical chemistry; sample preparation; liquid chromatography; mass spectrometry; proteomics; lipidomics; metabolomics; analytical method development; post-translational modifications of protein analysis; small molecule analysis for environmental and food analysis
Special Issues, Collections and Topics in MDPI journals

Dr. Carmela Maria Montone

E-Mail Website
Assistant Guest Editor

Department of Chemistry, SAPIENZA Università di Roma, P.le A. Moro 5, 00185 Rome, Italy
Interests: proteomics; peptidomics; protein extraction and purification; bioactive peptide analysis; method development and validation; lipidomics
Special Issues, Collections and Topics in MDPI journals

Dr. Andrea Cerrato

E-Mail Website
Assistant Guest Editor

Department of Chemistry, Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome, Italy
Interests: high-resolution mass spectrometry; hyphenated techniques; omics sciences; metabolomics; lipidomics; food analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Bottom–up proteomics is now an established filed. Today, thousands of proteins can be identified even from a single cell. The technological improvement in mass spectrometry (MS) provides increased resolution, acquisition speed, and enhanced tandem MS fragmentation capability via different techniques, which makes it possible to achieve such large-scale investigations. However, there are fields where sample preparation and chromatography are still fundamental to improve coverage and allow detection and identification of proteins and peptides. This is the case of protein post-translational modifications. In these areas, enrichment of modified peptides and proteins is still necessary to comply with very low abundance of such modifications and suppression during ionization.

In this context, this Special Issue covers all aspects of analytical improvements in sample preparation and analysis of proteins and peptides. Development of new approaches in protein extraction is encouraged, together with reports on the preparation of new phases for peptide and protein isolation or separation, for both sample preparation workflows, fractionation workflows or chromatographic separation. Finally, improvements and alternative strategies on peptide analysis by mass spectrometry and bioinformatics are also part of the Special Issue. Special attention will be devoted to methods specifically addressing low abundance or challenging post-translational modifications.

Dr. Susy Piovesana
Dr. Carmela Maria Montone
Dr. Andrea Cerrato
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

Proteomics
Peptidomics
Sample preparation
Protein post-translational modifications
Protein and peptide enrichment

Published Papers (12 papers)

Download All Papers

Research

Jump to: Review

9 pages, 648 KiB

Open AccessArticle

Comparison of LFQ and IPTL for Protein Identification and Relative Quantification

by Christina Johannsen, Christian J. Koehler and Bernd Thiede

Molecules 2021, 26(17), 5330; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26175330 - 02 Sep 2021

Cited by 1 | Viewed by 3579

Abstract

(1) Background: Mass spectrometry-based quantitative proteome profiling is most commonly performed by label-free quantification (LFQ), stable isotopic labeling with amino acids in cell culture (SILAC), and reporter ion-based isobaric labeling methods (TMT and iTRAQ). Isobaric peptide termini labeling (IPTL) was described as an alternative to these methods and is based on crosswise labeling of both peptide termini and MS2 quantification. High quantification accuracy was assumed for IPTL because multiple quantification points are obtained per identified MS2 spectrum. A direct comparison of IPTL with other quantification methods has not been performed yet because IPTL commonly requires digestion with endoproteinase Lys-C. (2) Methods: To enable tryptic digestion of IPTL samples, a novel labeling for IPTL was developed that combines metabolic labeling (Arg-0/Lys-0 and Arg-d4/Lys-d4, respectively) with crosswise N-terminal dimethylation (d4 and d0, respectively). (3) Results: The comparison of IPTL with LFQ revealed significantly more protein identifications for LFQ above homology ion scores but not above identity ion scores. (4) Conclusions: The quantification accuracy was superior for LFQ despite the many quantification points obtained with IPTL. Full article

(This article belongs to the Special Issue Advancements in Analytical Techniques for Proteomics)

► Show Figures

Graphical abstract

10 pages, 1032 KiB

Open AccessArticle

Detection of Intrinsically Resistant Candida in Mixed Samples by MALDI TOF-MS and a Modified Naïve Bayesian Classifier

by Jie Gong, Chong Shen, Meng Xiao, Huifang Zhang, Fei Zhao, Jiangzhong Zhang and Di Xiao

Molecules 2021, 26(15), 4470; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26154470 - 24 Jul 2021

Cited by 4 | Viewed by 1983

Abstract

MALDI-TOF MS is one of the major methods for clinical fungal identification, but it is currently only suitable for pure cultures of isolated strains. However, multiple fungal coinfections might occur in clinical practice. Some fungi involved in coinfection, such as Candida krusei and Candida auris, are intrinsically resistant to certain drugs. Identifying intrinsically resistant fungi from coinfected mixed cultures is extremely important for clinical treatment because different treatment options would be pursued accordingly. In this study, we counted the peaks of various species generated by Bruker Daltonik MALDI Biotyper software and accordingly constructed a modified naïve Bayesian classifier to analyze the presence of C. krusei and C. auris in simulated mixed samples. When reasonable parameters were fixed, the modified naïve Bayesian classifier effectively identified C. krusei and C. auris in the mixed samples (sensitivity 93.52%, specificity 92.5%). Our method not only provides a viable solution for identifying the two highlighted intrinsically resistant Candida species but also provides a case for the use of MALDI-TOF MS for analyzing coinfections of other species. Full article

(This article belongs to the Special Issue Advancements in Analytical Techniques for Proteomics)

► Show Figures

Figure 1

36 pages, 40435 KiB

Open AccessArticle

Quantitative Proteomics and Differential Protein Abundance Analysis after Depletion of Putative mRNA Receptors in the ER Membrane of Human Cells Identifies Novel Aspects of mRNA Targeting to the ER

by Pratiti Bhadra, Stefan Schorr, Monika Lerner, Duy Nguyen, Johanna Dudek, Friedrich Förster, Volkhard Helms, Sven Lang and Richard Zimmermann

Molecules 2021, 26(12), 3591; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26123591 - 11 Jun 2021

Cited by 11 | Viewed by 3390

Abstract

In human cells, one-third of all polypeptides enter the secretory pathway at the endoplasmic reticulum (ER). The specificity and efficiency of this process are guaranteed by targeting of mRNAs and/or polypeptides to the ER membrane. Cytosolic SRP and its receptor in the ER membrane facilitate the cotranslational targeting of most ribosome-nascent precursor polypeptide chain (RNC) complexes together with the respective mRNAs to the Sec61 complex in the ER membrane. Alternatively, fully synthesized precursor polypeptides are targeted to the ER membrane post-translationally by either the TRC, SND, or PEX19/3 pathway. Furthermore, there is targeting of mRNAs to the ER membrane, which does not involve SRP but involves mRNA- or RNC-binding proteins on the ER surface, such as RRBP1 or KTN1. Traditionally, the targeting reactions were studied in cell-free or cellular assays, which focus on a single precursor polypeptide and allow the conclusion of whether a certain precursor can use a certain pathway. Recently, cellular approaches such as proximity-based ribosome profiling or quantitative proteomics were employed to address the question of which precursors use certain pathways under physiological conditions. Here, we combined siRNA-mediated depletion of putative mRNA receptors in HeLa cells with label-free quantitative proteomics and differential protein abundance analysis to characterize RRBP1- or KTN1-involving precursors and to identify possible genetic interactions between the various targeting pathways. Furthermore, we discuss the possible implications on the so-called TIGER domains and critically discuss the pros and cons of this experimental approach. Full article

(This article belongs to the Special Issue Advancements in Analytical Techniques for Proteomics)

► Show Figures

Figure 1

16 pages, 2661 KiB

Open AccessArticle

Differential Glycosite Profiling—A Versatile Method to Compare Membrane Glycoproteomes

by Malwina Michalak, Martin Simon Kalteis, Aysel Ahadova, Matthias Kloor, Mark Kriegsmann, Katharina Kriegsmann, Uwe Warnken, Dominic Helm and Jürgen Kopitz

Molecules 2021, 26(12), 3564; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26123564 - 10 Jun 2021

Viewed by 1931

Abstract

Glycosylation is the most prevalent and varied form of post-translational protein modifications. Protein glycosylation regulates multiple cellular functions, including protein folding, cell adhesion, molecular trafficking and clearance, receptor activation, signal transduction, and endocytosis. In particular, membrane proteins are frequently highly glycosylated, which is both linked to physiological processes and of high relevance in various disease mechanisms. The cellular glycome is increasingly considered to be a therapeutic target. Here we describe a new strategy to compare membrane glycoproteomes, thereby identifying proteins with altered glycan structures and the respective glycosites. The workflow started with an optimized procedure for the digestion of membrane proteins followed by the lectin-based isolation of glycopeptides. Since alterations in the glycan part of a glycopeptide cause mass alterations, analytical size exclusion chromatography was applied to detect these mass shifts. N-glycosidase treatment combined with nanoUPLC-coupled mass spectrometry identified the altered glycoproteins and respective glycosites. The methodology was established using the colon cancer cell line CX1, which was treated with 2-deoxy-glucose—a modulator of N-glycosylation. The described methodology is not restricted to cell culture, as it can also be adapted to tissue samples or body fluids. Altogether, it is a useful module in various experimental settings that target glycan functions. Full article

(This article belongs to the Special Issue Advancements in Analytical Techniques for Proteomics)

► Show Figures

Graphical abstract

14 pages, 3131 KiB

Open AccessArticle

Effects of Kynurenic Acid on the Rat Aorta Ischemia—Reperfusion Model: Pharmacological Characterization and Proteomic Profiling

by Viviane Soares Souza Lima, Douglas Oscar Ceolin Mariano, Hugo Vigerelli, Sabrina Cardoso Janussi, Thayz Vanalli Lima Baptista, Mário Angelo Claudino, Daniel Carvalho Pimenta and Juliana Mozer Sciani

Molecules 2021, 26(10), 2845; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26102845 - 11 May 2021

Cited by 3 | Viewed by 1988

Abstract

Kynurenic acid (KYNA) is derived from tryptophan, formed by the kynurenic pathway. KYNA is being widely studied as a biomarker for neurological and cardiovascular diseases, as it is found in ischemic conditions as a protective agent; however, little is known about its effect after ischemia-reperfusion in the vascular system. We induced ischemia for 30 min followed by 5 min reperfusion (I/R) in the rat aorta for KYNA evaluation using functional assays combined with proteomics. KYNA recovered the exacerbated contraction induced by phenylephrine and relaxation induced by acetylcholine or sodium nitroprussiate in the I/R aorta, with vessel responses returning to values observed without I/R. The functional recovery can be related to the antioxidant activity of KYNA, which may be acting on the endothelium-injury prevention, especially during reperfusion, and to proteins that regulate neurotransmission and cell repair/growth, expressed after the KYNA treatment. These proteins interacted in a network, confirming a protein profile expression for endothelium and neuron repair after I/R. Thus, the KYNA treatment had the ability to recover the functionality of injured ischemic-reperfusion aorta, by tissue repairing and control of neurotransmitter release, which reinforces its role in the post-ischemic condition, and can be useful in the treatment of such disease. Full article

(This article belongs to the Special Issue Advancements in Analytical Techniques for Proteomics)

► Show Figures

Figure 1

16 pages, 11210 KiB

Open AccessCommunication

Discovery of Post-Translational Modifications in Emiliania huxleyi

by Van-An Duong, Onyou Nam, EonSeon Jin, Jong-Moon Park and Hookeun Lee

Molecules 2021, 26(7), 2027; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26072027 - 02 Apr 2021

Cited by 3 | Viewed by 2021

Abstract

Emiliania huxleyi is a cosmopolitan coccolithophore that plays an essential role in global carbon and sulfur cycling, and contributes to marine cloud formation and climate regulation. Previously, the proteomic profile of Emiliania huxleyi was investigated using a three-dimensional separation strategy combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS). The current study reuses the MS/MS spectra obtained, for the global discovery of post-translational modifications (PTMs) in this species without specific enrichment methods. Twenty-five different PTM types were examined using Trans-Proteomic Pipeline (Comet and PeptideProphet). Overall, 13,483 PTMs were identified in 7421 proteins. Methylation was the most frequent PTM with more than 2800 modified sites, and lysine was the most frequently modified amino acid with more than 4000 PTMs. The number of proteins identified increased by 22.5% to 18,780 after performing the PTM search. Compared to intact peptides, the intensities of some modified peptides were superior or equivalent. The intensities of some proteins increased dramatically after the PTM search. Gene ontology analysis revealed that protein persulfidation was related to photosynthesis in Emiliania huxleyi. Additionally, various membrane proteins were found to be phosphorylated. Thus, our global PTM discovery platform provides an overview of PTMs in the species and prompts further studies to uncover their biological functions. The combination of a three-dimensional separation method with global PTM search is a promising approach for the identification and discovery of PTMs in other species. Full article

(This article belongs to the Special Issue Advancements in Analytical Techniques for Proteomics)

► Show Figures

Graphical abstract

17 pages, 2344 KiB

Open AccessArticle

Biomarker Discovery of Acute Coronary Syndrome Using Proteomic Approach

by Miji Shin, Sang Hyun Park, Sora Mun, Jiyeong Lee and Hee-Gyoo Kang

Molecules 2021, 26(4), 1136; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26041136 - 20 Feb 2021

Cited by 4 | Viewed by 2020

Abstract

Acute coronary syndrome (ACS) is a condition in which the coronary artery supplying blood to the heart is infarcted via formation of a plaque and thrombus, resulting in abnormal blood supply and high mortality and morbidity. Therefore, the prompt and efficient diagnosis of ACS and the need for new ACS diagnostic biomarkers are important. In this study, we aimed to identify new ACS diagnostic biomarkers with high sensitivity and specificity using a proteomic approach. A discovery set with samples from 20 patients with ACS and 20 healthy controls was analyzed using mass spectrometry. Among the proteins identified, those showing a significant difference between each group were selected. Functional analysis of these proteins was conducted to confirm their association with functions in the diseased state. To determine ACS diagnostic biomarkers, standard peptides of the selected protein candidates from the discovery set were quantified, and these protein candidates were validated in a validation set consisting of the sera of 50 patients with ACS and 50 healthy controls. We showed that hemopexin, leucine-rich α-2-glycoprotein, and vitronectin levels were upregulated, whereas fibronectin level was downregulated, in patients with ACS. Thus, the use of these biomarkers may increase the accuracy of ACS diagnosis. Full article

(This article belongs to the Special Issue Advancements in Analytical Techniques for Proteomics)

► Show Figures

Figure 1

18 pages, 2570 KiB

Open AccessArticle

Synthesis and Matrix Properties of α-Cyano-5-phenyl-2,4-pentadienic Acid (CPPA) for Intact Proteins Analysis by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

by Antonio Monopoli, Angelo Nacci, Tommaso R. I. Cataldi and Cosima D. Calvano

Molecules 2020, 25(24), 6054; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25246054 - 21 Dec 2020

Cited by 7 | Viewed by 2907

Abstract

The effectiveness of a synthesized matrix, α-cyano-5-phenyl-2,4-pentadienic acid (CPPA), for protein analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in complex samples such as foodstuff and bacterial extracts, is demonstrated. Ultraviolet (UV) absorption along with laser desorption/ionization mass spectrometry (LDI-MS) experiments were systematically conducted in positive ion mode under standard Nd:YLF laser excitation with the aim of characterizing the matrix in terms of wavelength absorption and proton affinity. Besides, the results for standard proteins revealed that CPPA significantly enhanced the protein signals, reduced the spot-to-spot variability and increased the spot homogeneity. The CPPA matrix was successful employed to investigate intact microorganisms, milk and seed extracts for protein profiling. Compared to conventional matrices such as sinapinic acid (SA), α-cyano-4-hydroxycinnamic acid (CHCA) and 4-chloro-α-cyanocinnamic acid (CClCA), CPPA exhibited better signal-to-noise (S/N) ratios and a uniform response for most examined proteins occurring in milk, hazelnut and in intact bacterial cells of E. coli. These findings not only provide a reactive proton transfer MALDI matrix with excellent reproducibility and sensitivity, but also contribute to extending the battery of useful matrices for intact protein analysis. Full article

(This article belongs to the Special Issue Advancements in Analytical Techniques for Proteomics)

► Show Figures

Figure 1

19 pages, 1386 KiB

Open AccessArticle

Relative Abundance of Alpha-Amylase/Trypsin Inhibitors in Selected Sorghum Cultivars

by Sorel Tchewonpi Sagu, Eva Landgräber, Michal Rackiewicz, Gerd Huschek and Harshadrai Rawel

Molecules 2020, 25(24), 5982; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25245982 - 17 Dec 2020

Cited by 8 | Viewed by 6846

Abstract

Sorghum is of growing interest and considered as a safe food for wheat related disorders. Besides the gluten, α-amylase/trypsin-inhibitors (ATIs) have been identified as probable candidates for these disorders. Several studies focused on wheat-ATIs although there is still a lack of data referring to the relative abundance of sorghum-ATIs. The objective of this work was therefore to contribute to the characterization of sorghum ATI profiles by targeted proteomics tools. Fifteen sorghum cultivars from different regions were investigated with raw proteins ranging from 7.9 to 17.0 g/100 g. Ammonium bicarbonate buffer in combination with urea was applied for protein extraction, with concentration from 0.588 ± 0.047 to 4.140 ± 0.066 mg/mL. Corresponding electrophoresis data showed different protein profiles. UniProtKB data base research reveals two sorghum ATIs, P81367 and P81368; both reviewed and a targeted LC–MS/MS method was developed to analyze these. Quantifier peptides ELAAVPSR (P81367) and TYMVR (P81368) were identified and retained as biomarkers for relative quantification. Different reducing and alkylating agents were assessed and combination of tris (2 carboxyethyl) phosphine/iodoacetamide gave the best response. Linearity was demonstrated for the quantifier peptides with standard recovery between 92.2 and 107.6%. Nine sorghum cultivars presented up to 60 times lower ATI contents as compared to wheat samples. This data suggests that sorghum can effectively be considered as a good alternative to wheat. Full article

(This article belongs to the Special Issue Advancements in Analytical Techniques for Proteomics)

► Show Figures

Figure 1

13 pages, 2071 KiB

Open AccessArticle

Optimisation of Sporosori Purification and Protein Extraction Techniques for the Biotrophic Protozoan Plant Pathogen Spongospora subterranea

by Sadegh Balotf, Richard Wilson, Robert S. Tegg, David S. Nichols and Calum R. Wilson

Molecules 2020, 25(14), 3109; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25143109 - 08 Jul 2020

Cited by 9 | Viewed by 2841

Abstract

Spongospora subterranea is a soil-borne plant pathogen responsible for the economically significant root and powdery scab diseases of potato. However, the obligate biotrophic nature of S. subterranea has made the detailed study of the pathogen problematic. Here, we first compared the benefits of sporosori partial purification utilizing Ludox^® gradient centrifugation. We then undertook optimization efforts for protein isolation comparing the use of a urea buffer followed by single-pot solid-phase-enhanced sample preparation (SP3) and a sodium dodecyl sulphate (SDS) buffer followed by suspension-trapping (S-Trap). Label-free, quantitative proteomics was then used to evaluate the efficiency of the sporosori purification and the protein preparation methods. The purification protocol produced a highly purified suspension of S. subterranea sporosori without affecting the viability of the spores. The results indicated that the use of a combination of SDS and S-Trap for sample clean-up and digestion obtained a significantly higher number of identified proteins compared to using urea and SP3, with 218 and 652 proteins identified using the SP3 and S-Trap methods, respectively. The analysis of proteins by mass spectrometry showed that the number of identified proteins increased by approximately 40% after the purification of spores by Ludox^®. These results suggested a potential use of the described spore purification and protein preparation methods for the proteomics study of obligate biotrophic pathogens such as S. subterranea. Full article

(This article belongs to the Special Issue Advancements in Analytical Techniques for Proteomics)

► Show Figures

Graphical abstract

19 pages, 3457 KiB

Open AccessArticle

Proteomic Profiling of Emiliania huxleyi Using a Three-Dimensional Separation Method Combined with Tandem Mass Spectrometry

by Goyeun Yun, Jong-Moon Park, Van-An Duong, Jeong-Hun Mok, Jongho Jeon, Onyou Nam, Joonwon Lee, EonSeon Jin and Hookeun Lee

Molecules 2020, 25(13), 3028; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25133028 - 02 Jul 2020

Cited by 8 | Viewed by 3237

Abstract

Emiliania huxleyi is one of the most abundant marine planktons, and it has a crucial feature in the carbon cycle. However, proteomic analyses of Emiliania huxleyi have not been done extensively. In this study, a three-dimensional liquid chromatography (3D-LC) system consisting of strong cation exchange, high- and low-pH reversed-phase liquid chromatography was established for in-depth proteomic profiling of Emiliania huxleyi. From tryptic proteome digest, 70 fractions were generated and analyzed using liquid chromatography-tandem mass spectrometry. In total, more than 84,000 unique peptides and 10,000 proteins groups were identified with a false discovery rate of ≤0.01. The physicochemical properties of the identified peptides were evaluated. Using ClueGO, approximately 700 gene ontology terms and 15 pathways were defined from the identified protein groups with p-value ≤0.05, covering a wide range of biological processes, cellular components, and molecular functions. Many biological processes associated with CO₂ fixation, photosynthesis, biosynthesis, and metabolic process were identified. Various molecular functions relating to protein binding and enzyme activities were also found. The 3D-LC strategy is a powerful approach for comparative proteomic studies on Emiliania huxleyi to reveal changes in its protein level and related mechanism. Full article

(This article belongs to the Special Issue Advancements in Analytical Techniques for Proteomics)

► Show Figures

Graphical abstract

Review

Jump to: Research

13 pages, 1935 KiB

Open AccessReview

Current Analytical Strategies in Studying Chromatin-Associated-Proteome (Chromatome)

by Niamat Khan, Sidra Shahid and Abdul R. Asif

Molecules 2021, 26(21), 6694; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26216694 - 05 Nov 2021

Viewed by 2196

Abstract

Chromatin is a dynamic structure comprising of DNA and proteins. Its unique nature not only help to pack the DNA tightly within the cell but also is pivotal in regulating gene expression DNA replication. Furthermore it also protects the DNA from being damaged. Various proteins are involved in making a specific complex within a chromatin and the knowledge about these interacting partners is helpful to enhance our understanding about the pathophysiology of various chromatin associated diseases. Moreover, it could also help us to identify new drug targets and design more effective remedies. Due to the existence of chromatin in different forms under various physiological conditions it is hard to develop a single strategy to study chromatin associated proteins under all conditions. In our current review, we tried to provide an overview and comparative analysis of the strategies currently adopted to capture the DNA bounded protein complexes and their mass spectrometric identification and quantification. Precise information about the protein partners and their function in the DNA-protein complexes is crucial to design new and more effective therapeutic molecules against chromatin associated diseases. Full article

(This article belongs to the Special Issue Advancements in Analytical Techniques for Proteomics)

► Show Figures