ArticleMolecular & cellular proteomics : MCP2016
Opening a SWATH Window on Posttranslational Modifications: Automated Pursuit of Modified Peptides.
Article in Molecular & cellular proteomics : MCP, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 41 citations in OpenAlex.
- Coagulation factor IX analysis in bioreactor cell culture supernatant predicts quality of the purified product.Communications biology · 2021Article
- Phosphoproteomics Meets Chemical Genetics: Approaches for Global Mapping and Deciphering the Phosphoproteome.International journal of molecular sciences · 2020Review
- Review
- Clinically Relevant Post-Translational Modification Analyses-Maturing Workflows and Bioinformatics Tools.International journal of molecular sciences · 2018Review
- Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial.Molecular systems biology · 2018Review
- Precision Profiling of the Cardiovascular Post-Translationally Modified Proteome: Where There Is a Will, There Is a Way.Circulation research · 2018Review
- Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells.Methods in molecular biology (Clifton, N.J.) · 2018Article
- Comparative Analyses of Data Independent Acquisition Mass Spectrometric Approaches: DIA, WiSIM-DIA, and Untargeted DIA.Proteomics · 2018Article
- Monitoring of Plant Protein Post-translational Modifications Using Targeted Proteomics.Frontiers in plant science · 2018Review
- The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays.Journal of proteome research · 2017Article
- Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS.Nature biotechnology · 2017Article
- Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques.Expert review of proteomics · 2017Review
- Site-specific analysis of changes in the glycosylation of proteins in liver cirrhosis using data-independent workflow with soft fragmentation.Analytical and bioanalytical chemistry · 2017Article
- Mapping Biological Networks from Quantitative Data-Independent Acquisition Mass Spectrometry: Data to Knowledge Pipelines.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Highlights of the Biology and Disease-driven Human Proteome Project, 2015-2016.Journal of proteome research · 2016Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Posttranslational modifications of proteins play an important role in biology. For example, phosphorylation is a key component in signal transduction in all three domains of life, and histones can be modified in such a variety of ways that a histone code for gene regulation has been proposed. Shotgun proteomics is commonly used to identify posttranslational modifications as well as chemical modifications from sample processing. However, it favors the detection of abundant peptides over the repertoire presented, and the data analysis usually requires advance specification of modification masses and target amino acids, their number constrained by available computational resources. Recent advances in data independent acquisition mass spectrometry technologies such as SWATH-MS enable a deeper recording of the peptide contents of samples, including peptides with modifications. Here, we present a novel approach that applies the power of SWATH-MS analysis to the automated pursuit of modified peptides. With the new SWATHProphet(PTM) functionality added to the open source SWATHProphet software, precursor ions consistent with a modification are identified along with the mass and localization of the modification in the peptide sequence in a sensitive and unrestricted manner without the need to anticipate the modifications in advance. Using this method, we demonstrate the detection of a wide assortment of modified peptides, many unanticipated, in samples containing unpurified synthetic peptides and human urine, as well as in phospho-enriched human tissue culture cell samples.
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