ArticleJournal of proteome research2013
Improving peptide identification sensitivity in shotgun proteomics by stratification of search space.
Article in Journal of proteome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
14 citing papers in PubMed, 26 citations in OpenAlex.
- Mass spectrometry-based proteomics of FFPE tissues: progress, limitations, and clinical translation barriers.Clinical proteomics · 2025Review
- Metabolomic signatures of ideal cardiovascular health in black adults.Scientific reports · 2024Article
- Permafrost preservation reveals proteomic evidence for yak milk consumption in the 13Communications biology · 2023Article
- Investigation of Tryptic Protein Digestion in Microdroplets and in Bulk Solution.Journal of the American Society for Mass Spectrometry · 2022Article
- Identification of Antibiotic Resistance Proteins via MiCId's Augmented Workflow. A Mass Spectrometry-Based Proteomics Approach.Journal of the American Society for Mass Spectrometry · 2022Article
- Robust Accurate Identification and Biomass Estimates of Microorganisms via Tandem Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2020Article
- A precision medicine approach to defining the impact of doxorubicin on the bioenergetic-metabolite interactome in human platelets.Redox biology · 2020Article
- Nonspecific cleavages arising from reconstitution of trypsin under mildly acidic conditions.PloS one · 2020Article
- An Algorithm to Improve the Speed of Semi and Non-Specific Enzyme Searches in Proteomics.Current bioinformatics · 2020Article
- Mitochondria in precision medicine; linking bioenergetics and metabolomics in platelets.Redox biology · 2019Article
- Rapid Classification and Identification of Multiple Microorganisms with Accurate Statistical Significance via High-Resolution Tandem Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2018Article
- Proteomic evidence of dietary sources in ancient dental calculus.Proceedings. Biological sciences · 2018Article
- Tandem Mass Spectrum Identification via Cascaded Search.Journal of proteome research · 2015Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Because of its high specificity, trypsin is the enzyme of choice in shotgun proteomics. Nonetheless, several publications do report the identification of semitryptic and nontryptic peptides. Many of these peptides are thought to be signaling peptides or to have formed during sample preparation. It is known that only a small fraction of tandem mass spectra from a trypsin-digested protein mixture can be confidently matched to tryptic peptides. If other possibilities such as post-translational modifications and single-amino acid polymorphisms are ignored, this suggests that many unidentified spectra originate from semitryptic and nontryptic peptides. To include them in database searches, however, may not improve overall peptide identification because of the possible sensitivity reduction from search space expansion. To circumvent this issue for E-value-based search methods, we have designed a scheme that categorizes qualified peptides (i.e., peptides whose differences in molecular weight from the parent ion are within a specified error tolerance) into three tiers: tryptic, semitryptic, and nontryptic. This classification allows peptides that belong to different tiers to have different Bonferroni correction factors. Our results show that this scheme can significantly improve retrieval performance compared to those of search strategies that assign equal Bonferroni correction factors to all qualified peptides.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.