why high peptide fdr could result in low protein fdr may - why-did-fda-ban-peptides protein peptide

peptide-type-2 The intricate relationship between peptide and protein false discovery rates (FDR) is a critical aspect of modern proteomics. Understanding why high peptide FDR could result in low protein FDR is essential for accurate data interpretation in mass spectrometry-based studies. This article delves into the statistical underpinnings and practical implications of these interconnected error ratesTarget-Decoy Approach and False Discovery Rate.

Understanding False Discovery Rate (FDR)

The False Discovery Rate (FDR) is a statistical concept used to control the number of false positives in hypothesis testing. In proteomics, it's applied to assess the reliability of identified peptides and proteins. A low peptide FDR indicates a higher confidence in the identified peptides, meaning fewer of them are likely to be false positives. Conversely, a high peptide FDR suggests a greater proportion of false identifications at the peptide level.

The Interplay Between Peptide and Protein FDR

Proteins are typically identified in mass spectrometry experiments by inferring them from a set of detected peptides.A number of reasonscancause a PSM to be false, these include:Lowquality spectrum;;Peptidesnot in the database; and; Imperfect scoring function. To control ... This inference process is where the relationship between peptide FDR and protein FDR becomes crucial.作者：L Reiter·2009·被引用次数：378—For any PSM FDR, the ratio of decoy to target hits is higher for peptides and again higher for proteins. Unlike for the PSMs, this ratio is not to be mistaken ...

* High Peptide FDR Leading to Low Protein FDR: It might seem counterintuitive, but a high peptide FDR can sometimes lead to a low protein FDR. This scenario often arises when a protein is identified based on a large number of peptides, even if some of those peptides have a lower confidence score or a higher FDRTowards low false discovery rate estimation for protein- .... If a significant number of these peptides are true positives, their collective evidence can still strongly support the identification of the parent protein, resulting in a low protein FDR. As stated in one study, "this increase in error rate is a consequence of present proteins agglomerating more PSMs and peptides than spurious proteins." Essentially, the sheer volume of evidence at the peptide level can outweigh the noise from a high peptide FDR.

* The Role of Scoring and Thresholds: The scoring functions used in peptide identification assign a confidence score to each peptide-spectrum match (PSM). When a lower FDR threshold is applied, fewer peptides are accepted. However, if the scoring is robust, even with a high peptide FDR, the most confident peptides that pass the threshold might be sufficient to confidently identify a proteinA Scalable Approach for Protein False Discovery Rate .... Conversely, if the scoring function is imperfect or the spectrum quality is low, a high peptide FDR might indeed lead to a high protein FDR.

* Protein Inference Algorithms: The methods used for protein inference play a significant role.2016年3月5日—My understanding is that youcan't calculate anFDRfor a singleproteinbecause the dataset is too small for relevant statistics to be calculated. Some algorithms might require a minimum number of peptides or a certain level of spectral evidence to declare a protein identification.作者：Y Couté·2019·被引用次数：77—This observationcaneasily be explained: Withlower FDRthresholds, fewer decoys passed the threshold, and as aresult, the statistics were ... If a protein is supported by many peptides, the statistical confidence in its existence can be high, even if some of those peptides are false positives.A Scalable Approach for Protein False Discovery Rate ... This means that a high peptide FDR may not always translate directly to a problematic protein FDR.The False Discovery Rate (FDR) – an important statistical concept

* Decoy Databases and FDR Calculation: The target-decoy approach is a standard method for estimating FDR.Improved detection of differentially abundant proteins ... In this method, a "decoy" database of reversed or shuffled sequences is used.2024年6月9日—Most common mistakes when validating FDR include leaving protein- or peptide-level FDR filters activated in the software configuration and then ... The ratio of decoy hits to target hits at a given score threshold provides an estimate of the false discovery rate.Beyond target-decoy competition: stable validation of ... For peptides, the ratio of decoy to target hits is generally higher than for PSMs. For proteins, this ratio is again higher.2013年11月22日—Some peptide matches will be lost, which could lead to the loss of true proteins that had very low coverage, but the list of proteins with ... This means that controlling the FDR at the protein level often requires more stringent criteria or a larger number of confidently identified peptides.

Practical Implications and Recommendations

* Targeting 1% FDR: Most publications aim for a peptide FDR of 1% or betterA new estimation of protein-level false discovery rate. This is a common guideline for ensuring robust identifications at the peptide levelFalse Discovery Rate (FDR) Tutorial | Protein Identification. However, it's important to remember that a low peptide FDR doesn't automatically guarantee a low protein FDR.

* Impact of Data Quality: The quality of the mass spectrometry data is paramount.What does the different options mean in the Protein FDR field in the ... Low quality spectrum, peptides not in the database, and imperfect scoring functions can all contribute to a higher FDR at both the peptide and protein levels.

* Protein-Level FDR vsMultiple competition-based FDR control and its application .... Peptide-Level FDR: While peptide FDR is a measure of confidence in individual peptide identifications, protein-level FDR ensures the overall quality of the set of identified proteins. A protein might be inferred from several peptides, some high-confidence and some low-confidence. Protein-level FDR aims to control the rate of false protein identificationsAssessment of false discovery rate control in tandem mass ....

* Consideration of Protein Coverage: Proteins with very low coverage (few identified peptides) are more susceptible to being lost even if they are truly present, especially when stringent FDR filtering is applied. This is because the statistical evidence supporting their identification would be weak.

In conclusion, understanding why high peptide FDR could result in low protein FDR requires appreciating the statistical nuances of protein inference and the cumulative evidence provided by multiple peptides.Impact of peptide-to-spectrum match (PSM) false discovery... While a low peptide FDR is generally desirable, a high peptide FDR does not always necessitate a compromised protein FDR, particularly when a protein is supported by a substantial number of confidently identified peptides.作者：K Jeong·2012·被引用次数：212—...low(PSM-level)FDR may resultin excessive falsepeptideidentifications. Computing the empiricalpeptide-levelFDRis a readily-available ... Researchers must carefully consider the FDR at both levels and the methods employed for protein inference to ensure the validity of their proteomic findings.作者：O Serang·2015·被引用次数：59—proteinFDRs are actually not very meaningful because proteomics measurespeptidesnot proteins and the definition of a 'decoyprotein' is quite ...