ArticleJournal of proteome research2012
Automated selected reaction monitoring software for accurate label-free protein quantification.
Article in Journal of proteome research, 2012. 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.
- Targeted Selected Reaction Monitoring Verifies Histology Specific Peptide Signatures in Epithelial Ovarian Cancer.Cancers · 2021Article
- Deep neural network for detecting arbitrary precision peptide features through attention based segmentation.Scientific reports · 2021Article
- DeepIso: A Deep Learning Model for Peptide Feature Detection from LC-MS map.Scientific reports · 2019Article
- Application of targeted mass spectrometry in bottom-up proteomics for systems biology research.Journal of proteomics · 2018Review
- Quantitative proteomics analysis of cartilage response to mechanical injury and cytokine treatment.Matrix biology : journal of the International Society for Matrix Biology · 2017Article
- TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics.Nature methods · 2016Article
- Proteomic analysis of breast tumors confirms the mRNA intrinsic molecular subtypes using different classifiers: a large-scale analysis of fresh frozen tissue samples.Breast cancer research : BCR · 2016Article
- The clinical impact of recent advances in LC-MS for cancer biomarker discovery and verification.Expert review of proteomics · 2016Review
- Ranking Fragment Ions Based on Outlier Detection for Improved Label-Free Quantification in Data-Independent Acquisition LC-MS/MS.Journal of proteome research · 2015Article
- Representation of selected-reaction monitoring data in the mzQuantML data standard.Proteomics · 2015Article
- Article
- Numerical compression schemes for proteomics mass spectrometry data.Molecular & cellular proteomics : MCP · 2014Article
- An adaptive alignment algorithm for quality-controlled label-free LC-MS.Molecular & cellular proteomics : MCP · 2013Article
- File formats commonly used in mass spectrometry proteomics.Molecular & cellular proteomics : MCP · 2012Article
- Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes.Nature communications · 2012Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Selected reaction monitoring (SRM) is a mass spectrometry method with documented ability to quantify proteins accurately and reproducibly using labeled reference peptides. However, the use of labeled reference peptides becomes impractical if large numbers of peptides are targeted and when high flexibility is desired when selecting peptides. We have developed a label-free quantitative SRM workflow that relies on a new automated algorithm, Anubis, for accurate peak detection. Anubis efficiently removes interfering signals from contaminating peptides to estimate the true signal of the targeted peptides. We evaluated the algorithm on a published multisite data set and achieved results in line with manual data analysis. In complex peptide mixtures from whole proteome digests of Streptococcus pyogenes we achieved a technical variability across the entire proteome abundance range of 6.5-19.2%, which was considerably below the total variation across biological samples. Our results show that the label-free SRM workflow with automated data analysis is feasible for large-scale biological studies, opening up new possibilities for quantitative proteomics and systems biology.
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