Analysis of protein isoforms: Can we do it better?

Št́astná, Miroslava; Eyk, Jennifer E. Van

doi:10.1002/pmic.201200161

Cited by 64 publications

(63 citation statements)

References 105 publications

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“…Technological improvements, including the arrival of more accurate instruments, namely the quadrupole time-of-flight mass spectrometer (Q-TOF MS) (Morris et al 1996), resulted in the development of liquid chromatography-mass spectrometry (LC-MS) methodologies (Yergey 1990). These are powerful techniques that combine the physical separation capabilities of liquid chromatography with the mass analysis capabilities of mass spectrometry and that have consequently allowed for the identification of protein isoforms, which other gel-free methodologies do not permit (Baggerman et al 2005;Stastna and Van Eyk 2012).…”

Section: De Vs Modern Proteomicsmentioning

confidence: 99%

Proteome signatures—how are they obtained and what do they teach us?

Costa

Ferreira

Amado

et al. 2015

Appl Microbiol Biotechnol

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The dawn of a new Proteomics era, just over a decade ago, allowed for large-scale protein profiling studies that have been applied in the identification of distinctive molecular cell signatures. Proteomics provides a powerful approach for identifying and studying these multiple molecular markers in a vast array of biological systems, whether focusing on basic biological research, diagnosis, therapeutics, or systems biology. This is a continuously expanding field that relies on the combination of different methodologies and current advances, both technological and analytical, which have led to an explosion of protein signatures and biomarker candidates. But how are these biological markers obtained? And, most importantly, what can we learn from them? Herein, we briefly overview the currently available approaches for obtaining relevant information at the proteome level, while noting the current and future roles of both traditional and modern proteomics. Moreover, we provide some considerations on how the development of powerful and robust bioinformatics tools will greatly benefit high-throughput proteomics. Such strategies are of the utmost importance in the rapidly emerging field of immunoproteomics, which may play a key role in the identification of antigens with diagnostic and/or therapeutic potential and in the development of new vaccines. Finally, we consider the present limitations in the discovery of new signatures and biomarkers and speculate on how such hurdles may be overcome, while also offering a prospect for the next few years in what could be one of the most significant strategies in translational medicine research.

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Section: De Vs Modern Proteomicsmentioning

confidence: 99%

Proteome signatures—how are they obtained and what do they teach us?

Costa

Ferreira

Amado

et al. 2015

Appl Microbiol Biotechnol

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“…Proteoforms can arise from alternative splicing of mRNA, single amino acid polymorphisms, reading frame shifts, PTMs, or somatic recombinations, [36,47] and can have distinct biological functions. [48] Initially, proteoform mapping was based mainly on the differential mobility on 2DE.…”

Section: Ms-based Detection Of Proteoforms In Leishmaniamentioning

confidence: 99%

Proteomics and Leishmaniasis: Potential Clinical Applications

Capelli-Peixoto

Mule

Tano

et al. 2019

Proteomics Clinical Apps

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Leishmaniases are diseases caused by protozoan parasites of the genus Leishmania. They are endemic in 98 countries, affect around 12 million people worldwide and may present several distinct clinical forms. Unfortunately, there are only a few drugs available for treatment of leishmaniasis, which are toxic and not always effective. Different parasite species and different clinical forms require optimization of the treatment or more specific therapies, which are not available. The emergence of resistance is also a matter of concern. Besides, diagnosis can sometimes be complicated due to atypical manifestations and associations with other pathologies. In this review, proteomic data are presented and discussed in terms of their application in important issues in leishmaniasis such as parasite resistance to chemotherapy, diagnosis of active disease in patients and dogs, markers for different clinical forms, identification of virulence factors, and their potential use in vaccination. It is shown that proteomics has contributed to the discovery of potential biomarkers for prognosis, diagnosis, therapeutics, monitoring of disease progression, treatment follow‐up and identification of vaccine candidates for specific diseases. However, the authors believe its capabilities have not yet been fully explored for routine clinical analysis for several reasons, which will be presented in this review.

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“…Even though efforts have been made to identify and characterize protein isoforms , a comprehensive analysis of protein isoforms and subisoforms of cardiac myofilament proteins has been difficult due to the challenges of identification. This project aims to identify isoforms and subisoforms of the cardiac myofilament proteins in the myofilament‐enriched subproteome of rat cardiac tissue.…”

Section: Introductionmentioning

confidence: 99%

Identification of cardiac myofilament protein isoforms using multiple mass spectrometry based approaches

Kooij

Venkatraman

Kirk

et al. 2014

Proteomics Clinical Apps

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Purpose The identification of protein isoforms in complex biological samples is challenging. We, therefore, used a mass spectrometry (MS) approach to unambiguously identify cardiac myofilament protein isoforms based on the observation of a tryptic peptide consisting of a sequence unique to a particular isoform. Experimental design Three different workflows were used to isolate and fractionate rat cardiac myofilament subproteomes. All fractions were analyzed on an LTQ-Orbitrap MS, proteins were identified using various search engines (Mascot, X!Tandem, X!Tandem Kscore and OMSSA) with results combined via PepArML Meta-Search Engine, and a post-search analysis was performed by MASPECTRAS. Results The combination of multiple workflows and search engines resulted in a larger number of non-redundant proteins identified than with individual methods. A total of 102 myofilament annotated proteins were observed overlapping in two or three of the workflows. Literature search for myofilament presence with manual validation of the MS spectra was carried out for unambiguous identification: 10 cardiac myofilament and 17 cardiac myofilament-associated proteins were identified with 39 isoforms and sub-isoforms. Conclusion and clinical relevance We have identified multiple isoforms of myofilament proteins that are present in cardiac tissue using unique tryptic peptides. Changes in distribution of these protein isoforms under pathological conditions could ultimately allow for clinical diagnostics or as therapeutic targets.

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Analysis of protein isoforms: Can we do it better?

Cited by 64 publications

References 105 publications

Proteome signatures—how are they obtained and what do they teach us?

Proteome signatures—how are they obtained and what do they teach us?

Proteomics and Leishmaniasis: Potential Clinical Applications

Identification of cardiac myofilament protein isoforms using multiple mass spectrometry based approaches

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