Decoy|free protein|level false discovery rate estimation

Decoy-free protein-level false discovery rate estimation

In this article, we propose a decoy-free protein-level FDR estimation method. Under the null hypothesis that each candidate protein matches an identified ...

Decoy-free protein-level false discovery rate estimation - PubMed

In this article, we propose a decoy-free protein-level FDR estimation method. Under the null hypothesis that each candidate protein matches an identified ...

algorithm for decoy-free false discovery rate estimation in XL-MS/MS ...

We introduce a novel decoy-free framework for FDR estimation in XL-MS/MS. Our approach relies on multi-sample mixtures of skew normal distributions.

An algorithm for decoy-free false discovery rate estimation in XL-MS ...

... protein or from physically interacting proteins, thus improving our understanding of protein structure and function. To aid biological discovery ...

False discovery rate estimation using candidate peptides for each ...

However, when generating a protein-level decoy database, cTDS can estimate the FDR more accurately than TDS. For cTDS, the FDR can be ...

A Scalable Approach for Protein False Discovery Rate Estimation in ...

Calculating the number of confidently identified proteins and estimating false discovery rate (FDR) is a challenge when analyzing very large proteomic data ...

Repeat-Preserving Decoy Database for False Discovery Rate ...

... analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol. Cell. Proteomics 2011, 10 ...

Reanalysis of ProteomicsDB Using an Accurate, Sensitive, and ...

FDR, false discovery rate; TDS, target-decoy ... A scalable approach for protein false discovery rate estimation in large proteomic data sets.

Target-small decoy search strategy for false discovery rate estimation

One of the most important steps in peptide identification is to estimate the false discovery rate (FDR). The most commonly used method for ...

Mascot help: Automatic target-decoy searching and ... - Matrix Science

Protein FDR. Protein false discovery rate is estimated using a MAYU type of approach. Protein FDR estimation is always convoluted with protein inference, so ...

False Discovery Rate Estimation in Proteomics - BIOCEV

positive protein identifications (those that have a hit to the decoy database proteins) to that of the total number of protein identifica- tions mapping to ...

An algorithm for decoy-free false discovery rate estimation in XL-MS ...

Download Citation | An algorithm for decoy-free false discovery rate estimation in XL-MS/MS proteomics | Motivation Cross-linking tandem mass spectrometry ...

Target-decoy false discovery rate estimation using Crema - bioRxiv

Here we present Crema, an open source Python tool that im- plements several TDC methods of spectrum-, peptide- and protein-level FDR estimation.

False Discovery Rate (FDR) Tutorial | Protein Identification

At the same FDR, the best performer should identify the most PSMs. (Figure adopted from [1]). Estimating FDR with the Target-Decoy Method.

Decoy-free protein-level false discovery rate estimation - OUCI

Abstract Motivation: Statistical validation of protein identifications is an important issue in shotgun proteomics. The false discovery rate (FDR) is a ...

Common Decoy Distributions Simplify False Discovery Rate ...

In shotgun proteomics, false discovery rate (FDR) estimation is a necessary step to ensure the quality of accepted peptide-spectrum matches ...

Reanalysis of ProteomicsDB Using an Accurate, Sensitive, and ...

As this equally affects incorrect target and decoy PSMs, this should not lead to any biases for FDR estimation. Entrapment Searches. To assess if protein group- ...

Assessment of false discovery rate control in tandem mass ... - bioRxiv

We then apply several entrapment estimation methods to gauge the level of FDR control of four widely used tools for the analysis of data- ...

Artificial Decoy Spectral Libraries for False Discovery Rate ...

Abstract: The challenge of estimating false discovery rates. (FDR) in peptide identification from MS/MS spectra has received increased attention in ...

Overview of protein group-level FDR estimation methods, its ...

C, the razor peptide approach assigns a shared peptide to the protein group with the most unique identifications. D, the picked target-decoy strategy performs a ...