ArticleMolecular & cellular proteomics : MCP2014
Computing exact p-values for a cross-correlation shotgun proteomics score function.
Article in Molecular & cellular proteomics : MCP, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 1 of them a synthesis that pooled it.
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
27 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Soil and leaf litter metaproteomics-a brief guideline from sampling to understanding.FEMS microbiology ecology · 2016Guideline
- PyViscount: Validating False Discovery Rate Estimation Methods via Random Search Space Partition.Journal of proteome research · 2025Article
- Proteome-Wide Identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes.Nature communications · 2024Article
- The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data.Journal of proteome research · 2023Article
- Enhanced Proteomic Data Analysis with MetaMorpheus.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Improving Peptide-Level Mass Spectrometry Analysis via Double Competition.Journal of proteome research · 2022Article
- Morphine and high-fat diet differentially alter the gut microbiota composition and metabolic function in lean versus obese mice.ISME communications · 2022Article
- Considerations for constructing a protein sequence database for metaproteomics.Computational and structural biotechnology journal · 2022Review
- Averaging Strategy To Reduce Variability in Target-Decoy Estimates of False Discovery Rate.Journal of proteome research · 2019Article
- Joint Precursor Elution Profile Inference via Regression for Peptide Detection in Data-Independent Acquisition Mass Spectra.Journal of proteome research · 2019Article
- Bayesian Hierarchical Model for Protein Identifications.Journal of applied statistics · 2019Article
- Learning Concave Conditional Likelihood Models for Improved Analysis of Tandem Mass Spectra.Advances in neural information processing systems · 2018Article
- Combining High-Resolution and Exact Calibration To Boost Statistical Power: A Well-Calibrated Score Function for High-Resolution MS2 Data.Journal of proteome research · 2018Article
- Controlling the FDR in imperfect matches to an incomplete database.Journal of the American Statistical Association · 2018Article
- Gradients of Generative Models for Improved Discriminative Analysis of Tandem Mass Spectra.Advances in neural information processing systems · 2017Article
- Progressive calibration and averaging for tandem mass spectrometry statistical confidence estimation: Why settle for a single decoy?Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005- ) · 2017Article
- Multiplexed Post-Experimental Monoisotopic Mass Refinement (mPE-MMR) to Increase Sensitivity and Accuracy in Peptide Identifications from Tandem Mass Spectra of Cofragmentation.Analytical chemistry · 2017Article
- Effective Leveraging of Targeted Search Spaces for Improving Peptide Identification in Tandem Mass Spectrometry Based Proteomics.Journal of proteome research · 2015Article
- The SEQUEST family tree.Journal of the American Society for Mass Spectrometry · 2015Article
- A deeper look into Comet--implementation and features.Journal of the American Society for Mass Spectrometry · 2015Article
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.
Funding
Abstract
The core of every protein mass spectrometry analysis pipeline is a function that assesses the quality of a match between an observed spectrum and a candidate peptide. We describe a procedure for computing exact p-values for the oldest and still widely used score function, SEQUEST XCorr. The procedure uses dynamic programming to enumerate efficiently the full distribution of scores for all possible peptides whose masses are close to that of the spectrum precursor mass. Ranking identified spectra by p-value rather than XCorr significantly reduces variance because of spectrum-specific effects on the score. In combination with the Percolator postprocessor, the XCorr p-value yields more spectrum and peptide identifications at a fixed false discovery rate than Mascot, X!Tandem, Comet, and MS-GF+ across a variety of data sets.
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.