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Investigating protein isoforms via proteomics: a feasibility study.

ABSTRACT: Alternative splicing (AS) and processing of pre-messenger RNAs explains the discrepancy between the number of genes and proteome complexity in multicellular eukaryotic organisms. However, relatively few alternative protein isoforms have been experimentally identified, particularly at the protein level. In this study, we assess the ability of proteomics to inform on differently spliced protein isoforms in human and four other model eukaryotes. The number of Ensembl-annotated genes for which proteomic data exists that informs on AS exceeds 33% of the alternately spliced genes in the human and worm genomes. Examining AS in chicken via proteomics for the first time, we find support for over 600 AS genes. However, although peptide identifications support only a small fraction of alternative protein isoforms that are annotated in Ensembl, many more variants are amenable to proteomic identification. There remains a sizeable gap between these existing identifications (10-52% of AS genes) and those that are theoretically feasible (90-99%). We also compare annotations between Swiss-Prot and Ensembl, recommending use of both to maximize coverage of AS. We propose that targeted proteomic experiments using selected reactions and standards are essential to uncover further alternative isoforms and discuss the issues surrounding these strategies.

SUBMITTER: Blakeley P

PROVIDER: S-EPMC3708446 | biostudies-literature | 2010 Mar

REPOSITORIES: biostudies-literature

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Investigating protein isoforms via proteomics: a feasibility study.

Blakeley Paul P Siepen Jennifer A JA Lawless Craig C Hubbard Simon J SJ

Proteomics 20100301 6

Alternative splicing (AS) and processing of pre-messenger RNAs explains the discrepancy between the number of genes and proteome complexity in multicellular eukaryotic organisms. However, relatively few alternative protein isoforms have been experimentally identified, particularly at the protein level. In this study, we assess the ability of proteomics to inform on differently spliced protein isoforms in human and four other model eukaryotes. The number of Ensembl-annotated genes for which prote ...[more]

PMID: 20077415

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Project description:BackgroundProtein isoform generation, which may derive from alternative splicing, genetic polymorphism, and posttranslational modification, is an essential source of achieving molecular diversity by eukaryotic cells. Previous studies have shown that protein isoforms play critical roles in disease diagnosis, risk assessment, sub-typing, prognosis, and treatment outcome predictions. Understanding the types, presence, and abundance of different protein isoforms in different cellular and physiological conditions is a major task in functional proteomics, and may pave ways to molecular biomarker discovery of human diseases. In tandem mass spectrometry (MS/MS) based proteomics analysis, peptide peaks with exact matches to protein sequence records in the proteomics database may be identified with mass spectrometry (MS) search software. However, due to limited annotation and poor coverage of protein isoforms in proteomics databases, high throughput protein isoform identifications, particularly those arising from alternative splicing and genetic polymorphism, have not been possible.ResultsTherefore, we present the PEPtidomics Protein Isoform Database (PEPPI, http://bio.informatics.iupui.edu/peppi), a comprehensive database of computationally-synthesized human peptides that can identify protein isoforms derived from either alternatively spliced mRNA transcripts or SNP variations. We collected genome, pre-mRNA alternative splicing and SNP information from Ensembl. We synthesized in silico isoform transcripts that cover all exons and theoretically possible junctions of exons and introns, as well as all their variations derived from known SNPs. With three case studies, we further demonstrated that the database can help researchers discover and characterize new protein isoform biomarkers from experimental proteomics data.ConclusionsWe developed a new tool for the proteomics community to characterize protein isoforms from MS-based proteomics experiments. By cataloguing each peptide configurations in the PEPPI database, users can study genetic variations and alternative splicing events at the proteome level. They can also batch-download peptide sequences in FASTA format to search for MS/MS spectra derived from human samples. The database can help generate novel hypotheses on molecular risk factors and molecular mechanisms of complex diseases, leading to identification of potentially highly specific protein isoform biomarkers.

Project description:Advances in high-throughput mass spectrometry are making proteomics an increasingly important tool in genome annotation projects. Peptides detected in mass spectrometry experiments can be used to validate gene models and verify the translation of putative coding sequences (CDSs). Here, we have identified peptides that cover 35% of the genes annotated by the GENCODE consortium for the human genome as part of a comprehensive analysis of experimental spectra from two large publicly available mass spectrometry databases. We detected the translation to protein of "novel" and "putative" protein-coding transcripts as well as transcripts annotated as pseudogenes and nonsense-mediated decay targets. We provide a detailed overview of the population of alternatively spliced protein isoforms that are detectable by peptide identification methods. We found that 150 genes expressed multiple alternative protein isoforms. This constitutes the largest set of reliably confirmed alternatively spliced proteins yet discovered. Three groups of genes were highly overrepresented. We detected alternative isoforms for 10 of the 25 possible heterogeneous nuclear ribonucleoproteins, proteins with a key role in the splicing process. Alternative isoforms generated from interchangeable homologous exons and from short indels were also significantly enriched, both in human experiments and in parallel analyses of mouse and Drosophila proteomics experiments. Our results show that a surprisingly high proportion (almost 25%) of the detected alternative isoforms are only subtly different from their constitutive counterparts. Many of the alternative splicing events that give rise to these alternative isoforms are conserved in mouse. It was striking that very few of these conserved splicing events broke Pfam functional domains or would damage globular protein structures. This evidence of a strong bias toward subtle differences in CDS and likely conserved cellular function and structure is remarkable and strongly suggests that the translation of alternative transcripts may be subject to selective constraints.

Project description:IntroductionMillions of people survive injuries to the central or peripheral nervous system for which neurorehabilitation is required. In addition to the physical and cognitive impairments, many neurorehabilitation patients experience pain, often not widely recognised and inadequately treated. This is particularly true for multiple sclerosis (MS) patients, for whom pain is one of the most common symptoms. In clinical practice, pain assessment is usually conducted based on a subjective estimate. This approach can lead to inaccurate evaluations due to the influence of numerous factors, including emotional or cognitive aspects. To date, no objective and simple to use clinical methods allow objective quantification of pain and the diagnostic differentiation between the two main types of pain (nociceptive vs neuropathic). Wearable technologies and artificial intelligence (AI) have the potential to bridge this gap by continuously monitoring patients' health parameters and extracting meaningful information from them. Therefore, we propose to develop a new automatic AI-powered tool to assess pain and its characteristics during neurorehabilitation treatments using physiological signals collected by wearable sensors.Methods and analysisWe aim to recruit 15 participants suffering from MS undergoing physiotherapy treatment. During the study, participants will wear a wristband for three consecutive days and be monitored before and after their physiotherapy sessions. Measurement of traditionally used pain assessment questionnaires and scales (ie, painDETECT, Doleur Neuropathique 4 Questions, EuroQoL-5-dimension-3-level) and physiological signals (photoplethysmography, electrodermal activity, skin temperature, accelerometer data) will be collected. Relevant parameters from physiological signals will be identified, and AI algorithms will be used to develop automatic classification methods.Ethics and disseminationThe study has been approved by the local Ethical Committee (285-2022-SPER-AUSLBO). Participants are required to provide written informed consent. The results will be disseminated through contributions to international conferences and scientific journals, and they will also be included in a doctoral dissertation.Trial registration numberNCT05747040.

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Investigating protein isoforms via proteomics: a feasibility study.

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Investigating protein isoforms via proteomics: a feasibility study.

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