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Ananth V, Sanders J, Yilmaz M, Wen B, Oh S, Noble WS. A learned score function improves the power of mass spectrometry database search. Bioinformatics 2024; 40:i410-i417. [PMID: 38940129 PMCID: PMC11211853 DOI: 10.1093/bioinformatics/btae218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024] Open
Abstract
MOTIVATION One of the core problems in the analysis of protein tandem mass spectrometry data is the peptide assignment problem: determining, for each observed spectrum, the peptide sequence that was responsible for generating the spectrum. Two primary classes of methods are used to solve this problem: database search and de novo peptide sequencing. State-of-the-art methods for de novo sequencing use machine learning methods, whereas most database search engines use hand-designed score functions to evaluate the quality of a match between an observed spectrum and a candidate peptide from the database. We hypothesized that machine learning models for de novo sequencing implicitly learn a score function that captures the relationship between peptides and spectra, and thus may be re-purposed as a score function for database search. Because this score function is trained from massive amounts of mass spectrometry data, it could potentially outperform existing, hand-designed database search tools. RESULTS To test this hypothesis, we re-engineered Casanovo, which has been shown to provide state-of-the-art de novo sequencing capabilities, to assign scores to given peptide-spectrum pairs. We then evaluated the statistical power of this Casanovo score function, Casanovo-DB, to detect peptides on a benchmark of three mass spectrometry runs from three different species. In addition, we show that re-scoring with the Percolator post-processor benefits Casanovo-DB more than other score functions, further increasing the number of detected peptides.
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Affiliation(s)
- Varun Ananth
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - Justin Sanders
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - Melih Yilmaz
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - Bo Wen
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Sewoong Oh
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - William Stafford Noble
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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2
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O'Connor JD, Overton IM, McMahon SJ. Validation of In Vitro Trained Transcriptomic Radiosensitivity Signatures in Clinical Cohorts. Cancers (Basel) 2023; 15:3504. [PMID: 37444614 PMCID: PMC10340371 DOI: 10.3390/cancers15133504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/15/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Transcriptomic personalisation of radiation therapy has gained considerable interest in recent years. However, independent model testing on in vitro data has shown poor performance. In this work, we assess the reproducibility in clinical applications of radiosensitivity signatures. Agreement between radiosensitivity predictions from published signatures using different microarray normalization methods was assessed. Control signatures developed from resampled in vitro data were benchmarked in clinical cohorts. Survival analysis was performed using each gene in the clinical transcriptomic data, and gene set enrichment analysis was used to determine pathways related to model performance in predicting survival and recurrence. The normalisation approach impacted calculated radiosensitivity index (RSI) values. Indeed, the limits of agreement exceeded 20% with different normalisation approaches. No published signature significantly improved on the resampled controls for prediction of clinical outcomes. Functional annotation of gene models suggested that many overlapping biological processes are associated with cancer outcomes in RT treated and non-RT treated patients, including proliferation and immune responses. In summary, different normalisation methods should not be used interchangeably. The utility of published signatures remains unclear given the large proportion of genes relating to cancer outcome. Biological processes influencing outcome overlapped for patients treated with or without radiation suggest that existing signatures may lack specificity.
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Affiliation(s)
- John D O'Connor
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Ian M Overton
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Stephen J McMahon
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
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3
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Miura N, Okuda S. Current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics. Comput Struct Biotechnol J 2023; 21:1140-1150. [PMID: 36817962 PMCID: PMC9925844 DOI: 10.1016/j.csbj.2023.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/14/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023] Open
Abstract
Metaproteomics is a relatively young field that has only been studied for approximately 15 years. Nevertheless, it has the potential to play a key role in disease research by elucidating the mechanisms of communication between the human host and the microbiome. Although it has been useful in developing an understanding of various diseases, its analytical strategies remain limited to the extended application of proteomics. The sequence databases in metaproteomics must be large because of the presence of thousands of species in a typical sample, which causes problems unique to large databases. In this review, we demonstrate the usefulness of metaproteomics in disease research through examples from several studies. Additionally, we discuss the challenges of applying metaproteomics to conventional proteomics analysis methods and introduce studies that may provide clues to the solutions. We also discuss the need for a standard false discovery rate control method for metaproteomics to replace common target-decoy search approaches in proteomics and a method to ensure the reliability of peptide spectrum match.
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Affiliation(s)
- Nobuaki Miura
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, 2-5274 Gakkocho-dori, Chuo-ku, Niigata 951-8514, Japan
| | - Shujiro Okuda
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, 2-5274 Gakkocho-dori, Chuo-ku, Niigata 951-8514, Japan,Medical AI Center, Niigata University School of Medicine, 2-5274 Gakkocho-dori, Chuo-ku, Niigata 951-8514, Japan,Corresponding author at: Medical AI Center, Niigata University School of Medicine, 2-5274 Gakkocho-dori, Chuo-ku, Niigata 951-8514, Japan.
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4
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Couté Y, Bruley C, Burger T. Beyond Target-Decoy Competition: Stable Validation of Peptide and Protein Identifications in Mass Spectrometry-Based Discovery Proteomics. Anal Chem 2020; 92:14898-14906. [PMID: 32970414 DOI: 10.1021/acs.analchem.0c00328] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In bottom-up discovery proteomics, target-decoy competition (TDC) is the most popular method for false discovery rate (FDR) control. Despite unquestionable statistical foundations, this method has drawbacks, including its hitherto unknown intrinsic lack of stability vis-à-vis practical conditions of application. Although some consequences of this instability have already been empirically described, they may have been misinterpreted. This article provides evidence that TDC has become less reliable as the accuracy of modern mass spectrometers improved. We therefore propose to replace TDC by a totally different method to control the FDR at the spectrum, peptide, and protein levels, while benefiting from the theoretical guarantees of the Benjamini-Hochberg framework. As this method is simpler to use, faster to compute, and more stable than TDC, we argue that it is better adapted to the standardization and throughput constraints of current proteomic platforms.
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Affiliation(s)
- Yohann Couté
- Université Grenoble Alpes, CNRS, CEA, INSERM, IRIG, BGE, F-38000 Grenoble, France
| | - Christophe Bruley
- Université Grenoble Alpes, CNRS, CEA, INSERM, IRIG, BGE, F-38000 Grenoble, France
| | - Thomas Burger
- Université Grenoble Alpes, CNRS, CEA, INSERM, IRIG, BGE, F-38000 Grenoble, France
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5
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Harris AM, DeGiorgio M. Identifying and Classifying Shared Selective Sweeps from Multilocus Data. Genetics 2020; 215:143-171. [PMID: 32152048 PMCID: PMC7198270 DOI: 10.1534/genetics.120.303137] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/29/2020] [Indexed: 11/18/2022] Open
Abstract
Positive selection causes beneficial alleles to rise to high frequency, resulting in a selective sweep of the diversity surrounding the selected sites. Accordingly, the signature of a selective sweep in an ancestral population may still remain in its descendants. Identifying signatures of selection in the ancestor that are shared among its descendants is important to contextualize the timing of a sweep, but few methods exist for this purpose. We introduce the statistic SS-H12, which can identify genomic regions under shared positive selection across populations and is based on the theory of the expected haplotype homozygosity statistic H12, which detects recent hard and soft sweeps from the presence of high-frequency haplotypes. SS-H12 is distinct from comparable statistics because it requires a minimum of only two populations, and properly identifies and differentiates between independent convergent sweeps and true ancestral sweeps, with high power and robustness to a variety of demographic models. Furthermore, we can apply SS-H12 in conjunction with the ratio of statistics we term [Formula: see text] and [Formula: see text] to further classify identified shared sweeps as hard or soft. Finally, we identified both previously reported and novel shared sweep candidates from human whole-genome sequences. Previously reported candidates include the well-characterized ancestral sweeps at LCT and SLC24A5 in Indo-Europeans, as well as GPHN worldwide. Novel candidates include an ancestral sweep at RGS18 in sub-Saharan Africans involved in regulating the platelet response and implicated in sudden cardiac death, and a convergent sweep at C2CD5 between European and East Asian populations that may explain their different insulin responses.
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Affiliation(s)
- Alexandre M Harris
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802
- Molecular, Cellular, and Integrative Biosciences at the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida 33431
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6
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Sulimov P, Kertész-Farkas A. Tailor: A Nonparametric and Rapid Score Calibration Method for Database Search-Based Peptide Identification in Shotgun Proteomics. J Proteome Res 2020; 19:1481-1490. [DOI: 10.1021/acs.jproteome.9b00736] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Pavel Sulimov
- Department of Data Analysis and Artificial Intelligence, Faculty of Computer Science, National Research University Higher School of Economics (HSE), 11 Pokrovsky Boulevard, Moscow 109028, Russian Federation
| | - Attila Kertész-Farkas
- Department of Data Analysis and Artificial Intelligence, Faculty of Computer Science, National Research University Higher School of Economics (HSE), 11 Pokrovsky Boulevard, Moscow 109028, Russian Federation
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7
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Keich U, Tamura K, Noble WS. Averaging Strategy To Reduce Variability in Target-Decoy Estimates of False Discovery Rate. J Proteome Res 2019; 18:585-593. [PMID: 30560673 DOI: 10.1021/acs.jproteome.8b00802] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Decoy database search with target-decoy competition (TDC) provides an intuitive, easy-to-implement method for estimating the false discovery rate (FDR) associated with spectrum identifications from shotgun proteomics data. However, the procedure can yield different results for a fixed data set analyzed with different decoy databases, and this decoy-induced variability is particularly problematic for smaller FDR thresholds, data sets, or databases. The average TDC (aTDC) protocol combats this problem by exploiting multiple independently shuffled decoy databases to provide an FDR estimate with reduced variability. We provide a tutorial introduction to aTDC, describe an improved variant of the protocol that offers increased statistical power, and discuss how to deploy aTDC in practice using the Crux software toolkit.
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Affiliation(s)
- Uri Keich
- School of Mathematics and Statistics F07 , University of Sydney , Sydney , New South Wales 2006 , Australia
| | - Kaipo Tamura
- Department of Genome Sciences , University of Washington , Foege Building S220B, 3720 15th Avenue NE , Seattle , Washington 98195-5065 , United States
| | - William Stafford Noble
- Department of Genome Sciences , University of Washington , Foege Building S220B, 3720 15th Avenue NE , Seattle , Washington 98195-5065 , United States.,Department of Computer Science and Engineering , University of Washington , Seattle , Washington 98195-5065 , United States
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8
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Halloran JT, Rocke DM. Learning Concave Conditional Likelihood Models for Improved Analysis of Tandem Mass Spectra. ADVANCES IN NEURAL INFORMATION PROCESSING SYSTEMS 2018; 31:5420-5430. [PMID: 31745383 PMCID: PMC6863516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The most widely used technology to identify the proteins present in a complex biological sample is tandem mass spectrometry, which quickly produces a large collection of spectra representative of the peptides (i.e., protein subsequences) present in the original sample. In this work, we greatly expand the parameter learning capabilities of a dynamic Bayesian network (DBN) peptide-scoring algorithm, Didea [25], by deriving emission distributions for which its conditional log-likelihood scoring function remains concave. We show that this class of emission distributions, called Convex Virtual Emissions (CVEs), naturally generalizes the log-sum-exp function while rendering both maximum likelihood estimation and conditional maximum likelihood estimation concave for a wide range of Bayesian networks. Utilizing CVEs in Didea allows efficient learning of a large number of parameters while ensuring global convergence, in stark contrast to Didea's previous parameter learning framework (which could only learn a single parameter using a costly grid search) and other trainable models [12, 13, 14] (which only ensure convergence to local optima). The newly trained scoring function substantially outperforms the state-of-the-art in both scoring function accuracy and downstream Fisher kernel analysis. Furthermore, we significantly improve Didea's runtime performance through successive optimizations to its message passing schedule and derive explicit connections between Didea's new concave score and related MS/MS scoring functions.
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Affiliation(s)
- John T Halloran
- Department of Public Health Sciences University of California, Davis,
| | - David M Rocke
- Department of Public Health Sciences University of California, Davis,
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9
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Cammarata MB, Macias LA, Rosenberg J, Bolufer A, Brodbelt JS. Expanding the Scope of Cross-Link Identifications by Incorporating Collisional Activated Dissociation and Ultraviolet Photodissociation Methods. Anal Chem 2018; 90:6385-6389. [PMID: 29722964 PMCID: PMC6040644 DOI: 10.1021/acs.analchem.7b04009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
With the advent of new cross-linking chemistries, analytical technologies, and search algorithms, cross-linking has become an increasingly popular strategy for evaluating tertiary and quaternary structures of proteins. Collisional activated dissociation remains the primary MS/MS method for identifications of peptide cross-links in high throughput workflows. Ultraviolet photodissociation (UVPD) at 193 nm has emerged as an alternative ion activation method well-suited for characterization of peptides and has been found in some cases to identify different peptides or provide distinctive sequence information than obtained by collisional activation methods. Complementary high energy collision dissociation (HCD) and UVPD were used in the present study to characterize protein cross-linking for bovine serum albumin, hemoglobin, and E. coli ribosome. Cross-links identified by HCD and UVPD using bis(sulfosuccinimidyl)suberate (BS3), a homobifunctional amine-to-amine cross-linker, and 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMTMM), a heterofunctional amine-to-carboxylic acid cross-linker, were evaluated in the present study. While more unique BS3 cross-links were identified by HCD, UVPD, and HCD provided a complementary panel of DMTMM cross-links which extended the degree of structural insight obtained for the proteins.
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Affiliation(s)
- Michael B Cammarata
- Department of Chemistry , University of Texas Austin , Texas 78712 , United States
| | - Luis A Macias
- Department of Chemistry , University of Texas Austin , Texas 78712 , United States
| | - Jake Rosenberg
- Department of Chemistry , University of Texas Austin , Texas 78712 , United States
| | - Alexander Bolufer
- Department of Chemistry , University of Texas Austin , Texas 78712 , United States
| | - Jennifer S Brodbelt
- Department of Chemistry , University of Texas Austin , Texas 78712 , United States
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10
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Ghodrati F, Mehrabian M, Williams D, Halgas O, Bourkas MEC, Watts JC, Pai EF, Schmitt-Ulms G. The prion protein is embedded in a molecular environment that modulates transforming growth factor β and integrin signaling. Sci Rep 2018; 8:8654. [PMID: 29872131 PMCID: PMC5988664 DOI: 10.1038/s41598-018-26685-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/14/2018] [Indexed: 01/06/2023] Open
Abstract
At times, it can be difficult to discern if a lack of overlap in reported interactions for a protein-of-interest reflects differences in methodology or biology. In such instances, systematic analyses of protein-protein networks across diverse paradigms can provide valuable insights. Here, we interrogated the interactome of the prion protein (PrP), best known for its central role in prion diseases, in four mouse cell lines. Analyses made use of identical affinity capture and sample processing workflows. Negative controls were generated from PrP knockout lines of the respective cell models, and the relative levels of peptides were quantified using isobaric labels. The study uncovered 26 proteins that reside in proximity to PrP. All of these proteins are predicted to have access to the outer face of the plasma membrane, and approximately half of them were not reported to interact with PrP before. Strikingly, although several proteins exhibited profound co-enrichment with PrP in a given model, except for the neural cell adhesion molecule 1, no protein was highly enriched in all PrP-specific interactomes. However, Gene Ontology analyses revealed a shared association of the majority of PrP candidate interactors with cellular events at the intersection of transforming growth factor β and integrin signaling.
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Affiliation(s)
- Farinaz Ghodrati
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, Ontario, M5T 0S8, Canada.,Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Mohadeseh Mehrabian
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, Ontario, M5T 0S8, Canada.,Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Declan Williams
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, Ontario, M5T 0S8, Canada
| | - Ondrej Halgas
- Department of Biochemistry, University of Toronto, Medical Sciences Building, 5th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Matthew E C Bourkas
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, Ontario, M5T 0S8, Canada.,Department of Biochemistry, University of Toronto, Medical Sciences Building, 5th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Joel C Watts
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, Ontario, M5T 0S8, Canada.,Department of Biochemistry, University of Toronto, Medical Sciences Building, 5th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Emil F Pai
- Department of Biochemistry, University of Toronto, Medical Sciences Building, 5th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.,Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer Research Tower, 101 College Street, Toronto, Ontario, M5G 1L7, Canada
| | - Gerold Schmitt-Ulms
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, Ontario, M5T 0S8, Canada. .,Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
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11
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Zhang T, Meng L, Kong W, Yin Z, Wang Y, Schneider JD, Chen S. Quantitative proteomics reveals a role of JAZ7 in plant defense response to Pseudomonas syringae DC3000. J Proteomics 2018; 175:114-126. [DOI: 10.1016/j.jprot.2018.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 11/15/2017] [Accepted: 01/02/2018] [Indexed: 12/11/2022]
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12
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Antonov I, Marakhonov A, Zamkova M, Medvedeva Y. ASSA: Fast identification of statistically significant interactions between long RNAs. J Bioinform Comput Biol 2018; 16:1840001. [PMID: 29375012 DOI: 10.1142/s0219720018400012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The discovery of thousands of long noncoding RNAs (lncRNAs) in mammals raises a question about their functionality. It has been shown that some of them are involved in post-transcriptional regulation of other RNAs and form inter-molecular duplexes with their targets. Sequence alignment tools have been used for transcriptome-wide prediction of RNA-RNA interactions. However, such approaches have poor prediction accuracy since they ignore RNA's secondary structure. Application of the thermodynamics-based algorithms to long transcripts is not computationally feasible on a large scale. Here, we describe a new computational pipeline ASSA that combines sequence alignment and thermodynamics-based tools for efficient prediction of RNA-RNA interactions between long transcripts. To measure the hybridization strength, the sum energy of all the putative duplexes is computed. The main novelty implemented in ASSA is the ability to quickly estimate the statistical significance of the observed interaction energies. Most of the functional hybridizations between long RNAs were classified as statistically significant. ASSA outperformed 11 other tools in terms of the Area Under the Curve on two out of four test sets. Additionally, our results emphasized a unique property of the [Formula: see text] repeats with respect to the RNA-RNA interactions in the human transcriptome. ASSA is available at https://sourceforge.net/projects/assa/.
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Affiliation(s)
- Ivan Antonov
- * Institute of Bioengineering, Federal Research Center Fundamentals of Biotechnology RAS, Moscow 117312, Russia.,† Department of Molecular and Biological Physics & Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
| | - Andrey Marakhonov
- ‡ Laboratory of Functional Analysis of the Genome, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia.,§ Federal State Scientific Budgetary Institution, Research Centre for Medical Genetics, Moscow 115478, Russia
| | - Maria Zamkova
- ¶ Russian N.N. Blokhin Cancer Research Center, Moscow 115478, Russia
| | - Yulia Medvedeva
- * Institute of Bioengineering, Federal Research Center Fundamentals of Biotechnology RAS, Moscow 117312, Russia.,† Department of Molecular and Biological Physics & Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia.,∥ Vavilov Institute of General Genetics, RAS, Moscow 119333, Russia
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13
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Keich U, Noble WS. 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- ) 2017; 10229:99-116. [PMID: 29326989 PMCID: PMC5758044 DOI: 10.1007/978-3-319-56970-3_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Estimating the false discovery rate (FDR) among a list of tandem mass spectrum identifications is mostly done through target-decoy competition (TDC). Here we offer two new methods that can use an arbitrarily small number of additional randomly drawn decoy databases to improve TDC. Specifically, "Partial Calibration" utilizes a new meta-scoring scheme that allows us to gradually benefit from the increase in the number of identifications calibration yields and "Averaged TDC" (a-TDC) reduces the liberal bias of TDC for small FDR values and its variability throughout. Combining a-TDC with "Progressive Calibration" (PC), which attempts to find the "right" number of decoys required for calibration we see substantial impact in real datasets: when analyzing the Plasmodium falciparum data it typically yields almost the entire 17% increase in discoveries that "full calibration" yields (at FDR level 0.05) using 60 times fewer decoys. Our methods are further validated using a novel realistic simulation scheme and importantly, they apply more generally to the problem of controlling the FDR among discoveries from searching an incomplete database.
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Affiliation(s)
- Uri Keich
- School of Mathematics and Statistics F07, University of Sydney
| | - William Stafford Noble
- Department of Genome Sciences, Department of Computer Science and Engineering, University of Washington
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14
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Alves G, Yu YK. Confidence assignment for mass spectrometry based peptide identifications via the extreme value distribution. Bioinformatics 2016; 32:2642-9. [PMID: 27153659 DOI: 10.1093/bioinformatics/btw225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 04/16/2016] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION There is a growing trend for biomedical researchers to extract evidence and draw conclusions from mass spectrometry based proteomics experiments, the cornerstone of which is peptide identification. Inaccurate assignments of peptide identification confidence thus may have far-reaching and adverse consequences. Although some peptide identification methods report accurate statistics, they have been limited to certain types of scoring function. The extreme value statistics based method, while more general in the scoring functions it allows, demands accurate parameter estimates and requires, at least in its original design, excessive computational resources. Improving the parameter estimate accuracy and reducing the computational cost for this method has two advantages: it provides another feasible route to accurate significance assessment, and it could provide reliable statistics for scoring functions yet to be developed. RESULTS We have formulated and implemented an efficient algorithm for calculating the extreme value statistics for peptide identification applicable to various scoring functions, bypassing the need for searching large random databases. AVAILABILITY AND IMPLEMENTATION The source code, implemented in C ++ on a linux system, is available for download at ftp://ftp.ncbi.nlm.nih.gov/pub/qmbp/qmbp_ms/RAId/RAId_Linux_64Bit CONTACT yyu@ncbi.nlm.nih.gov SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gelio Alves
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Yi-Kuo Yu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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15
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Eng JK, Hoopmann MR, Jahan TA, Egertson JD, Noble WS, MacCoss MJ. A deeper look into Comet--implementation and features. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1865-74. [PMID: 26115965 PMCID: PMC4607604 DOI: 10.1007/s13361-015-1179-x] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/22/2015] [Accepted: 04/27/2015] [Indexed: 05/04/2023]
Abstract
The Comet database search software was initially released as an open source project in late 2012. Prior to that, Comet existed as the University of Washington's academic version of the SEQUEST database search tool. Despite its availability and widespread use over the years, some details about its implementation have not been previously disseminated or are not well understood. We address a few of these details in depth and highlight new features available in the latest release. Comet is freely available for download at http://comet-ms.sourceforge.net or it can be accessed as a component of a number of larger software projects into which it has been incorporated. Graphical Abstract ᅟ.
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Affiliation(s)
- Jimmy K Eng
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | | | - Tahmina A Jahan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jarrett D Egertson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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16
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Abstract
Analysis pipelines that assign peptides to shotgun proteomics mass spectra often discard identified spectra deemed irrelevant to the scientific hypothesis being tested. To improve statistical power, I propose that researchers remove irrelevant peptides from the database prior to searching rather than assigning these peptides to spectra and then discarding the matches.
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17
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Akhtar MN, Southey BR, Andrén PE, Sweedler JV, Rodriguez-Zas SL. Identification of best indicators of peptide-spectrum match using a permutation resampling approach. J Bioinform Comput Biol 2015; 12:1440001. [PMID: 25362838 DOI: 10.1142/s0219720014400010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Various indicators of observed-theoretical spectrum matches were compared and the resulting statistical significance was characterized using permutation resampling. Novel decoy databases built by resampling the terminal positions of peptide sequences were evaluated to identify the conditions for accurate computation of peptide match significance levels. The methodology was tested on real and manually curated tandem mass spectra from peptides across a wide range of sizes. Spectra match indicators from complementary database search programs were profiled and optimal indicators were identified. The combination of the optimal indicator and permuted decoy databases improved the calculation of the peptide match significance compared to the approaches currently implemented in the database search programs that rely on distributional assumptions. Permutation tests using p-values obtained from software-dependent matching scores and E-values outperformed permutation tests using all other indicators. The higher overlap in matches between the database search programs when using end permutation compared to existing approaches confirmed the superiority of the end permutation method to identify peptides. The combination of effective match indicators and the end permutation method is recommended for accurate detection of peptides.
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Affiliation(s)
- Malik N Akhtar
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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18
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Abstract
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Accurate
assignment of peptide sequences to observed fragmentation
spectra is hindered by the large number of hypotheses that must be
considered for each observed spectrum. A high score assigned to a
particular peptide–spectrum match (PSM) may not end up being
statistically significant after multiple testing correction. Researchers
can mitigate this problem by controlling the hypothesis space in various
ways: considering only peptides resulting from enzymatic cleavages,
ignoring possible post-translational modifications or single nucleotide
variants, etc. However, these strategies sacrifice identifications
of spectra generated by rarer types of peptides. In this work, we
introduce a statistical testing framework, cascade search, that directly
addresses this problem. The method requires that the user specify a priori a statistical confidence threshold as well as a
series of peptide databases. For instance, such a cascade of databases
could include fully tryptic, semitryptic, and nonenzymatic peptides
or peptides with increasing numbers of modifications. Cascaded search
then gradually expands the list of candidate peptides from more likely
peptides toward rare peptides, sequestering at each stage any spectrum
that is identified with a specified statistical confidence. We compare
cascade search to a standard procedure that lumps all of the peptides
into a single database, as well as to a previously described group
FDR procedure that computes the FDR separately within each database.
We demonstrate, using simulated and real data, that cascade search
identifies more spectra at a fixed FDR threshold than with either
the ungrouped or grouped approach. Cascade search thus provides a
general method for maximizing the number of identified spectra in
a statistically rigorous fashion.
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Affiliation(s)
- Attila Kertesz-Farkas
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States.,School of Mathematics and Statistics, University of Sydney, Camperdown, NSW 2006, Australia.,Department of Genome Sciences, Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Uri Keich
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States.,School of Mathematics and Statistics, University of Sydney, Camperdown, NSW 2006, Australia.,Department of Genome Sciences, Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States.,School of Mathematics and Statistics, University of Sydney, Camperdown, NSW 2006, Australia.,Department of Genome Sciences, Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
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19
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Keich U, Noble WS. On the importance of well-calibrated scores for identifying shotgun proteomics spectra. J Proteome Res 2014; 14:1147-60. [PMID: 25482958 PMCID: PMC4324453 DOI: 10.1021/pr5010983] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Identifying
the peptide responsible for generating an observed
fragmentation spectrum requires scoring a collection of candidate
peptides and then identifying the peptide that achieves the highest
score. However, analysis of a large collection of such spectra requires
that the score assigned to one spectrum be well-calibrated with respect
to the scores assigned to other spectra. In this work, we define the
notion of calibration in the context of shotgun proteomics spectrum
identification, and we introduce a simple, albeit computationally
intensive, technique to calibrate an arbitrary score function. We
demonstrate that this calibration procedure yields an increased number
of identified spectra at a fixed false discovery rate (FDR) threshold.
We also show that proper calibration of scores has a surprising effect
on a previously described FDR estimation procedure, making the procedure
less conservative. Finally, we provide empirical results suggesting
that even partial calibration, which is much less computationally
demanding, can yield significant increases in spectrum identification.
Overall, we argue that accurate shotgun proteomics analysis requires
careful attention to score calibration.
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Affiliation(s)
- Uri Keich
- School of Mathematics and Statistics F07, University of Sydney , NSW 2006, Australia
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20
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Accurate assignment of significance to neuropeptide identifications using Monte Carlo k-permuted decoy databases. PLoS One 2014; 9:e111112. [PMID: 25329667 PMCID: PMC4201571 DOI: 10.1371/journal.pone.0111112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 09/26/2014] [Indexed: 12/18/2022] Open
Abstract
In support of accurate neuropeptide identification in mass spectrometry experiments, novel Monte Carlo permutation testing was used to compute significance values. Testing was based on k-permuted decoy databases, where k denotes the number of permutations. These databases were integrated with a range of peptide identification indicators from three popular open-source database search software (OMSSA, Crux, and X! Tandem) to assess the statistical significance of neuropeptide spectra matches. Significance p-values were computed as the fraction of the sequences in the database with match indicator value better than or equal to the true target spectra. When applied to a test-bed of all known manually annotated mouse neuropeptides, permutation tests with k-permuted decoy databases identified up to 100% of the neuropeptides at p-value < 10(-5). The permutation test p-values using hyperscore (X! Tandem), E-value (OMSSA) and Sp score (Crux) match indicators outperformed all other match indicators. The robust performance to detect peptides of the intuitive indicator "number of matched ions between the experimental and theoretical spectra" highlights the importance of considering this indicator when the p-value was borderline significant. Our findings suggest permutation decoy databases of size 1×105 are adequate to accurately detect neuropeptides and this can be exploited to increase the speed of the search. The straightforward Monte Carlo permutation testing (comparable to a zero order Markov model) can be easily combined with existing peptide identification software to enable accurate and effective neuropeptide detection. The source code is available at http://stagbeetle.animal.uiuc.edu/pepshop/MSMSpermutationtesting.
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21
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Wang J, Bourne PE, Bandeira N. MixGF: spectral probabilities for mixture spectra from more than one peptide. Mol Cell Proteomics 2014; 13:3688-97. [PMID: 25225354 DOI: 10.1074/mcp.o113.037218] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In large-scale proteomic experiments, multiple peptide precursors are often cofragmented simultaneously in the same mixture tandem mass (MS/MS) spectrum. These spectra tend to elude current computational tools because of the ubiquitous assumption that each spectrum is generated from only one peptide. Therefore, tools that consider multiple peptide matches to each MS/MS spectrum can potentially improve the relatively low spectrum identification rate often observed in proteomics experiments. More importantly, data independent acquisition protocols promoting the cofragmentation of multiple precursors are emerging as alternative methods that can greatly improve the throughput of peptide identifications but their success also depends on the availability of algorithms to identify multiple peptides from each MS/MS spectrum. Here we address a fundamental question in the identification of mixture MS/MS spectra: determining the statistical significance of multiple peptides matched to a given MS/MS spectrum. We propose the MixGF generating function model to rigorously compute the statistical significance of peptide identifications for mixture spectra and show that this approach improves the sensitivity of current mixture spectra database search tools by a ≈30-390%. Analysis of multiple data sets with MixGF reveals that in complex biological samples the number of identified mixture spectra can be as high as 20% of all the identified spectra and the number of unique peptides identified only in mixture spectra can be up to 35.4% of those identified in single-peptide spectra.
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Affiliation(s)
- Jian Wang
- From the ‡Bioinformatics Program, University of California, San Diego, La Jolla, California
| | - Philip E Bourne
- §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California
| | - Nuno Bandeira
- §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California; ¶Center for Computational Mass Spectrometry, University of California, San Diego, La, Jolla, California; ‖Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92092
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22
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Howbert JJ, Noble WS. Computing exact p-values for a cross-correlation shotgun proteomics score function. Mol Cell Proteomics 2014; 13:2467-79. [PMID: 24895379 DOI: 10.1074/mcp.o113.036327] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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.
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Affiliation(s)
- J Jeffry Howbert
- From the ‡Department of Genome Sciences, University of Washington, Seattle, Washington
| | - William Stafford Noble
- From the ‡Department of Genome Sciences, University of Washington, Seattle, Washington; §Department of Computer Science and Engineering, University of Washington, Seattle, Washington
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23
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Bollineni RC, Hoffmann R, Fedorova M. Proteome-wide profiling of carbonylated proteins and carbonylation sites in HeLa cells under mild oxidative stress conditions. Free Radic Biol Med 2014; 68:186-95. [PMID: 24321318 DOI: 10.1016/j.freeradbiomed.2013.11.030] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 11/14/2013] [Accepted: 11/27/2013] [Indexed: 12/11/2022]
Abstract
A number of oxidative protein modifications have been well characterized during the past decade. Presumably, reversible oxidative posttranslational modifications (PTMs) play a significant role in redox signaling pathways, whereas irreversible modifications including reactive protein carbonyl groups are harmful, as their levels are typically increased during aging and in certain diseases. Despite compelling evidence linking protein carbonylation to numerous disorders, the underlying molecular mechanisms at the proteome remain to be identified. Recent advancements in analysis of PTMs by mass spectrometry provided new insights into the mechanisms of protein carbonylation, such as protein susceptibility and exact modification sites, but only for a limited number of proteins. Here we report the first proteome-wide study of carbonylated proteins including modification sites in HeLa cells for mild oxidative stress conditions. The analysis relied on our recent strategy utilizing mass spectrometry-based enrichment of carbonylated peptides after DNPH derivatization. Thus a total of 210 carbonylated proteins containing 643 carbonylation sites were consistently identified in three replicates. Most carbonylation sites (284, 44.2%) resulted from oxidation of lysine residues (aminoadipic semialdehyde). Additionally, 121 arginine (18.8%), 121 threonine (18.8%), and 117 proline residues (18.2%) were oxidized to reactive carbonyls. The sequence motifs were significantly enriched for lysine and arginine residues near carbonylation sites (±10 residues). Gene Ontology analysis revealed that 80% of the carbonylated proteins originated from organelles, 50% enrichment of which was demonstrated for the nucleus. Moreover, functional interactions between carbonylated proteins of kinetochore/spindle machinery and centrosome organization were significantly enriched. One-third of the 210 carbonylated proteins identified here are regulated during apoptosis.
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Affiliation(s)
- Ravi Chand Bollineni
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Faculty of Chemistry and Mineralogy, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Ralf Hoffmann
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Faculty of Chemistry and Mineralogy, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Maria Fedorova
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Faculty of Chemistry and Mineralogy, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany.
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24
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Granholm V, Kim S, Navarro JCF, Sjölund E, Smith RD, Käll L. Fast and accurate database searches with MS-GF+Percolator. J Proteome Res 2013; 13:890-7. [PMID: 24344789 DOI: 10.1021/pr400937n] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
One can interpret fragmentation spectra stemming from peptides in mass-spectrometry-based proteomics experiments using so-called database search engines. Frequently, one also runs post-processors such as Percolator to assess the confidence, infer unique peptides, and increase the number of identifications. A recent search engine, MS-GF+, has shown promising results, due to a new and efficient scoring algorithm. However, MS-GF+ provides few statistical estimates about the peptide-spectrum matches, hence limiting the biological interpretation. Here, we enabled Percolator processing for MS-GF+ output and observed an increased number of identified peptides for a wide variety of data sets. In addition, Percolator directly reports p values and false discovery rate estimates, such as q values and posterior error probabilities, for peptide-spectrum matches, peptides, and proteins, functions that are useful for the whole proteomics community.
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Affiliation(s)
- Viktor Granholm
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University , Solna, Sweden
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25
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Shao W, Zhu K, Lam H. Refining similarity scoring to enable decoy-free validation in spectral library searching. Proteomics 2013; 13:3273-83. [DOI: 10.1002/pmic.201300232] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 08/06/2013] [Accepted: 09/10/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Wenguang Shao
- Division of Biomedical Engineering; The Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Kan Zhu
- Department of Chemical and Biomolecular Engineering; The Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Henry Lam
- Division of Biomedical Engineering; The Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
- Department of Chemical and Biomolecular Engineering; The Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
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26
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Alves G, Yu YK. Improving peptide identification sensitivity in shotgun proteomics by stratification of search space. J Proteome Res 2013; 12:2571-81. [PMID: 23668635 DOI: 10.1021/pr301139y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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.
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Affiliation(s)
- Gelio Alves
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
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27
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Granholm V, Navarro JF, Noble WS, Käll L. Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics. J Proteomics 2012; 80:123-31. [PMID: 23268117 DOI: 10.1016/j.jprot.2012.12.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Revised: 11/30/2012] [Accepted: 12/11/2012] [Indexed: 01/10/2023]
Abstract
The analysis of a shotgun proteomics experiment results in a list of peptide-spectrum matches (PSMs) in which each fragmentation spectrum has been matched to a peptide in a database. Subsequently, most protein inference algorithms rank peptides according to the best-scoring PSM for each peptide. However, there is disagreement in the scientific literature on the best method to assess the statistical significance of the resulting peptide identifications. Here, we use a previously described calibration protocol to evaluate the accuracy of three different peptide-level statistical confidence estimation procedures: the classical Fisher's method, and two complementary procedures that estimate significance, respectively, before and after selecting the top-scoring PSM for each spectrum. Our experiments show that the latter method, which is employed by MaxQuant and Percolator, produces the most accurate, well-calibrated results.
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Affiliation(s)
- Viktor Granholm
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - José Fernández Navarro
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology (KTH), Solna, Sweden
| | - William Stafford Noble
- Department of Genome Sciences, Department of Computer Science and Engineering, University of Washington, USA
| | - Lukas Käll
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology (KTH), Solna, Sweden.
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28
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Li Q, Eng JK, Stephens M. A likelihood-based scoring method for peptide identification using mass spectrometry. Ann Appl Stat 2012. [DOI: 10.1214/12-aoas568] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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29
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McIlwain S, Mathews M, Bereman MS, Rubel EW, MacCoss MJ, Noble WS. Estimating relative abundances of proteins from shotgun proteomics data. BMC Bioinformatics 2012; 13:308. [PMID: 23164367 PMCID: PMC3599300 DOI: 10.1186/1471-2105-13-308] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 10/31/2012] [Indexed: 11/10/2022] Open
Abstract
Background Spectral counting methods provide an easy means of identifying proteins with differing abundances between complex mixtures using shotgun proteomics data. The crux spectral-counts command, implemented as part of the Crux software toolkit, implements four previously reported spectral counting methods, the spectral index (SIN), the exponentially modified protein abundance index (emPAI), the normalized spectral abundance factor (NSAF), and the distributed normalized spectral abundance factor (dNSAF). Results We compared the reproducibility and the linearity relative to each protein’s abundance of the four spectral counting metrics. Our analysis suggests that NSAF yields the most reproducible counts across technical and biological replicates, and both SIN and NSAF achieve the best linearity. Conclusions With the crux spectral-counts command, Crux provides open-source modular methods to analyze mass spectrometry data for identifying and now quantifying peptides and proteins. The C++ source code, compiled binaries, spectra and sequence databases are available at
http://noble.gs.washington.edu/proj/crux-spectral-counts.
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Affiliation(s)
- Sean McIlwain
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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30
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Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles). Proteomics Clin Appl 2012; 5:580-9. [PMID: 22213554 DOI: 10.1002/prca.201100097] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development and deployment of methods for measuring and documenting data quality metrics. On September 18, 2010, the U.S. National Cancer Institute (NCI) convened the "International Workshop on Proteomic Data Quality Metrics" in Sydney, Australia, to identify and address issues facing the development and use of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed and agreed up on two primary needs for the wide use of quality metrics: (i) an evolving list of comprehensive quality metrics and (ii) standards accompanied by software analytics. Attendees stressed the importance of increased education and training programs to promote reliable protocols in proteomics. This workshop report explores the historic precedents, key discussions, and necessary next steps to enhance the quality of open access data. By agreement, this article is published simultaneously in Proteomics, Proteomics Clinical Applications, Journal of Proteome Research, and Molecular and Cellular Proteomics, as a public service to the research community. The peer review process was a coordinated effort conducted by a panel of referees selected by the journals.
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Affiliation(s)
- Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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31
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32
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Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). J Proteome Res 2012; 11:1412-9. [PMID: 22053864 PMCID: PMC3272102 DOI: 10.1021/pr201071t] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development and deployment of methods for measuring and documenting data quality metrics. On September 18, 2010, the U.S. National Cancer Institute (NCI) convened the "International Workshop on Proteomic Data Quality Metrics" in Sydney, Australia, to identify and address issues facing the development and use of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed and agreed up on two primary needs for the wide use of quality metrics: (1) an evolving list of comprehensive quality metrics and (2) standards accompanied by software analytics. Attendees stressed the importance of increased education and training programs to promote reliable protocols in proteomics. This workshop report explores the historic precedents, key discussions, and necessary next steps to enhance the quality of open access data. By agreement, this article is published simultaneously in the Journal of Proteome Research, Molecular and Cellular Proteomics, Proteomics, and Proteomics Clinical Applications as a public service to the research community. The peer review process was a coordinated effort conducted by a panel of referees selected by the journals.
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Affiliation(s)
- Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States.
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33
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Breidenbach MA, Palaniappan KK, Pitcher AA, Bertozzi CR. Mapping yeast N-glycosites with isotopically recoded glycans. Mol Cell Proteomics 2012; 11:M111.015339. [PMID: 22261724 PMCID: PMC3433913 DOI: 10.1074/mcp.m111.015339] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Asparagine-linked glycosylation is a common post-translational modification of proteins; in addition to participating in key macromolecular interactions, N-glycans contribute to protein folding, trafficking, and stability. Despite their importance, few N-glycosites have been experimentally mapped in the Saccharomyces cerevisiae proteome. Factors including glycan heterogeneity, low abundance, and low occupancy can complicate site mapping. Here, we report a novel mass spectrometry-based strategy for detection of N-glycosites in the yeast proteome. Our method imparts N-glycopeptide mass envelopes with a pattern that is computationally distinguishable from background ions. Isotopic recoding is achieved via metabolic incorporation of a defined mixture of N-acetylglucosamine isotopologs into N-glycans. Peptides bearing the recoded envelopes are specifically targeted for fragmentation, facilitating high confidence site mapping. This strategy requires no chemical modification of the N-glycans or stringent sample enrichment. Further, enzymatically simplified N-glycans are preserved on peptides. Using this approach, we identify 133 N-glycosites spanning 58 proteins, nearly doubling the number of experimentally observed N-glycosites in the yeast proteome.
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Affiliation(s)
- Mark A Breidenbach
- Department of Chemistry, Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA
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34
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Abstract
High-throughput proteomics experiments involving tandem mass spectrometry produce large volumes of complex data that require sophisticated computational analyses. As such, the field offers many challenges for computational biologists. In this article, we briefly introduce some of the core computational and statistical problems in the field and then describe a variety of outstanding problems that readers of PLoS Computational Biology might be able to help solve.
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Affiliation(s)
- William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
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35
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Eisenacher M, Kohl M, Turewicz M, Koch MH, Uszkoreit J, Stephan C. Search and decoy: the automatic identification of mass spectra. Methods Mol Biol 2012; 893:445-488. [PMID: 22665317 DOI: 10.1007/978-1-61779-885-6_28] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In recent years, the generation and interpretation of MS/MS spectra for the identification of peptides and proteins has matured to a frequently used automatic workflow in Proteomics. Several software solutions for the automated analysis of MS/MS spectra allow for high-throughput/high-performance analyses of complex samples. Related to MS/MS searches, target-decoy approaches have gained more and more popularity: in a "decoy" part of the search database nonexistent sequences mimic real sequences (the "target" sequences). With their help, the number of falsely identified peptides/proteins can be estimated after a search and the resulting protein list can be cut at a specified false discovery rate (FDR). This is an essential prerequisite for all quantitative approaches, as they rely on correct identifications. Especially the label-free approach "spectral counting"-gaining more and more popularity due to low costs and simplicity-depends directly on the correctness of peptide-spectrum matches (PSMs). This work's aim is to describe five popular search engines-especially their general properties regarding protein identification, but also their quantification abilities, if those go beyond spectral counting. By doing so, Proteomics researchers are enabled to compare their features and to choose an appropriate solution for their specific question. Furthermore, the search engines are applied to a spectrum data set generated from a complex sample with a Thermo LTQ Velos OrbiTrap (Thermo Fisher Scientific, Waltham, MA, USA). The results of the search engines are compared, e.g., regarding time requirements, peptides and proteins found, and the search engines' behavior using the decoy approach.
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Affiliation(s)
- Martin Eisenacher
- Department of Medical Proteomics/Bioanalytics, Medizinishchces Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany.
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Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles). Proteomics 2011; 12:11-20. [PMID: 22069307 DOI: 10.1002/pmic.201100562] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 10/27/2011] [Indexed: 11/10/2022]
Abstract
Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development and deployment of methods for measuring and documenting data quality metrics. On September 18, 2010, the U.S. National Cancer Institute (NCI) convened the "International Workshop on Proteomic Data Quality Metrics" in Sydney, Australia, to identify and address issues facing the development and use of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed and agreed upon two primary needs for the wide use of quality metrics: (i) an evolving list of comprehensive quality metrics and (ii) standards accompanied by software analytics. Attendees stressed the importance of increased education and training programs to promote reliable protocols in proteomics. This workshop report explores the historic precedents, key discussions, and necessary next steps to enhance the quality of open access data. By agreement, this article is published simultaneously in Proteomics, Proteomics Clinical Applications, Journal of Proteome Research, and Molecular and Cellular Proteomics, as a public service to the research community. The peer review process was a coordinated effort conducted by a panel of referees selected by the journals.
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Affiliation(s)
- Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Shteynberg D, Deutsch EW, Lam H, Eng JK, Sun Z, Tasman N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI. iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol Cell Proteomics 2011; 10:M111.007690. [PMID: 21876204 PMCID: PMC3237071 DOI: 10.1074/mcp.m111.007690] [Citation(s) in RCA: 412] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 08/03/2011] [Indexed: 11/06/2022] Open
Abstract
The combination of tandem mass spectrometry and sequence database searching is the method of choice for the identification of peptides and the mapping of proteomes. Over the last several years, the volume of data generated in proteomic studies has increased dramatically, which challenges the computational approaches previously developed for these data. Furthermore, a multitude of search engines have been developed that identify different, overlapping subsets of the sample peptides from a particular set of tandem mass spectrometry spectra. We present iProphet, the new addition to the widely used open-source suite of proteomic data analysis tools Trans-Proteomics Pipeline. Applied in tandem with PeptideProphet, it provides more accurate representation of the multilevel nature of shotgun proteomic data. iProphet combines the evidence from multiple identifications of the same peptide sequences across different spectra, experiments, precursor ion charge states, and modified states. It also allows accurate and effective integration of the results from multiple database search engines applied to the same data. The use of iProphet in the Trans-Proteomics Pipeline increases the number of correctly identified peptides at a constant false discovery rate as compared with both PeptideProphet and another state-of-the-art tool Percolator. As the main outcome, iProphet permits the calculation of accurate posterior probabilities and false discovery rate estimates at the level of sequence identical peptide identifications, which in turn leads to more accurate probability estimates at the protein level. Fully integrated with the Trans-Proteomics Pipeline, it supports all commonly used MS instruments, search engines, and computer platforms. The performance of iProphet is demonstrated on two publicly available data sets: data from a human whole cell lysate proteome profiling experiment representative of typical proteomic data sets, and from a set of Streptococcus pyogenes experiments more representative of organism-specific composite data sets.
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Affiliation(s)
| | | | - Henry Lam
- §Department of Chemical and Biomolecular Engineering, the Hong Kong University of Science and Technology, Hong Kong
| | - Jimmy K. Eng
- ¶Department of Genome Sciences, University of Washington, Seattle, WA
| | - Zhi Sun
- From the ‡Institute for Systems Biology, Seattle, WA
| | | | - Luis Mendoza
- From the ‡Institute for Systems Biology, Seattle, WA
| | | | - Ruedi Aebersold
- ‖Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- **Faculty of Sciences, University of Zurich, Zurich, Switzerland
- ‡‡Center for Systems Physiology and Metabolic Diseases, Zurich Switzerland
| | - Alexey I. Nesvizhskii
- §§Department of Pathology, University of Michigan, Ann Arbor, MI
- ¶¶Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
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38
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Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). Mol Cell Proteomics 2011; 10:O111.015446. [PMID: 22052993 DOI: 10.1074/mcp.o111.015446] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development and deployment of methods for measuring and documenting data quality metrics. On September 18, 2010, the United States National Cancer Institute convened the "International Workshop on Proteomic Data Quality Metrics" in Sydney, Australia, to identify and address issues facing the development and use of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed and agreed up on two primary needs for the wide use of quality metrics: 1) an evolving list of comprehensive quality metrics and 2) standards accompanied by software analytics. Attendees stressed the importance of increased education and training programs to promote reliable protocols in proteomics. This workshop report explores the historic precedents, key discussions, and necessary next steps to enhance the quality of open access data. By agreement, this article is published simultaneously in the Journal of Proteome Research, Molecular and Cellular Proteomics, Proteomics, and Proteomics Clinical Applications as a public service to the research community. The peer review process was a coordinated effort conducted by a panel of referees selected by the journals.
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Affiliation(s)
- Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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Eng JK, Searle BC, Clauser KR, Tabb DL. A face in the crowd: recognizing peptides through database search. Mol Cell Proteomics 2011; 10:R111.009522. [PMID: 21876205 PMCID: PMC3226415 DOI: 10.1074/mcp.r111.009522] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 07/19/2011] [Indexed: 12/31/2022] Open
Abstract
Peptide identification via tandem mass spectrometry sequence database searching is a key method in the array of tools available to the proteomics researcher. The ability to rapidly and sensitively acquire tandem mass spectrometry data and perform peptide and protein identifications has become a commonly used proteomics analysis technique because of advances in both instrumentation and software. Although many different tandem mass spectrometry database search tools are currently available from both academic and commercial sources, these algorithms share similar core elements while maintaining distinctive features. This review revisits the mechanism of sequence database searching and discusses how various parameter settings impact the underlying search.
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Affiliation(s)
- Jimmy K Eng
- University of Washington, Department of Genome Sciences, Seattle, WA 98195, USA.
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Spirin V, Shpunt A, Seebacher J, Gentzel M, Shevchenko A, Gygi S, Sunyaev S. Assigning spectrum-specific P-values to protein identifications by mass spectrometry. ACTA ACUST UNITED AC 2011; 27:1128-34. [PMID: 21349864 DOI: 10.1093/bioinformatics/btr089] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MOTIVATION Although many methods and statistical approaches have been developed for protein identification by mass spectrometry, the problem of accurate assessment of statistical significance of protein identifications remains an open question. The main issues are as follows: (i) statistical significance of inferring peptide from experimental mass spectra must be platform independent and spectrum specific and (ii) individual spectrum matches at the peptide level must be combined into a single statistical measure at the protein level. RESULTS We present a method and software to assign statistical significance to protein identifications from search engines for mass spectrometric data. The approach is based on asymptotic theory of order statistics. The parameters of the asymptotic distributions of identification scores are estimated for each spectrum individually. The method relies on new unbiased estimators for parameters of extreme value distribution. The estimated parameters are used to assign a spectrum-specific P-value to each peptide-spectrum match. The protein-level confidence measure combines P-values of peptide-to-spectrum matches. CONCLUSION We extensively tested the method using triplicate mouse and yeast high-throughput proteomic experiments. The proposed statistical approach improves the sensitivity of protein identifications without compromising specificity. While the method was primarily designed to work with Mascot, it is platform-independent and is applicable to any search engine which outputs a single score for a peptide-spectrum match. We demonstrate this by testing the method in conjunction with X!Tandem. AVAILABILITY The software is available for download at ftp://genetics.bwh.harvard.edu/SSPV/. CONTACT ssunyaev@rics.bwh.harvard.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Victor Spirin
- Division of Genetics, Brigham and Women's Hospital, Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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41
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Granholm V, Käll L. Quality assessments of peptide-spectrum matches in shotgun proteomics. Proteomics 2011; 11:1086-93. [DOI: 10.1002/pmic.201000432] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 10/05/2010] [Accepted: 11/02/2010] [Indexed: 11/06/2022]
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RAId_aPS: MS/MS analysis with multiple scoring functions and spectrum-specific statistics. PLoS One 2010; 5:e15438. [PMID: 21103371 PMCID: PMC2982831 DOI: 10.1371/journal.pone.0015438] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 09/20/2010] [Indexed: 11/26/2022] Open
Abstract
Statistically meaningful comparison/combination of peptide identification results from various search methods is impeded by the lack of a universal statistical standard. Providing an -value calibration protocol, we demonstrated earlier the feasibility of translating either the score or heuristic -value reported by any method into the textbook-defined -value, which may serve as the universal statistical standard. This protocol, although robust, may lose spectrum-specific statistics and might require a new calibration when changes in experimental setup occur. To mitigate these issues, we developed a new MS/MS search tool, RAId_aPS, that is able to provide spectrum-specific-values for additive scoring functions. Given a selection of scoring functions out of RAId score, K-score, Hyperscore and XCorr, RAId_aPS generates the corresponding score histograms of all possible peptides using dynamic programming. Using these score histograms to assign -values enables a calibration-free protocol for accurate significance assignment for each scoring function. RAId_aPS features four different modes: (i) compute the total number of possible peptides for a given molecular mass range, (ii) generate the score histogram given a MS/MS spectrum and a scoring function, (iii) reassign -values for a list of candidate peptides given a MS/MS spectrum and the scoring functions chosen, and (iv) perform database searches using selected scoring functions. In modes (iii) and (iv), RAId_aPS is also capable of combining results from different scoring functions using spectrum-specific statistics. The web link is http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/raid_aps/index.html. Relevant binaries for Linux, Windows, and Mac OS X are available from the same page.
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43
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Nesvizhskii AI. A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteomics 2010; 73:2092-123. [PMID: 20816881 DOI: 10.1016/j.jprot.2010.08.009] [Citation(s) in RCA: 358] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 08/25/2010] [Accepted: 08/25/2010] [Indexed: 12/18/2022]
Abstract
This manuscript provides a comprehensive review of the peptide and protein identification process using tandem mass spectrometry (MS/MS) data generated in shotgun proteomic experiments. The commonly used methods for assigning peptide sequences to MS/MS spectra are critically discussed and compared, from basic strategies to advanced multi-stage approaches. A particular attention is paid to the problem of false-positive identifications. Existing statistical approaches for assessing the significance of peptide to spectrum matches are surveyed, ranging from single-spectrum approaches such as expectation values to global error rate estimation procedures such as false discovery rates and posterior probabilities. The importance of using auxiliary discriminant information (mass accuracy, peptide separation coordinates, digestion properties, and etc.) is discussed, and advanced computational approaches for joint modeling of multiple sources of information are presented. This review also includes a detailed analysis of the issues affecting the interpretation of data at the protein level, including the amplification of error rates when going from peptide to protein level, and the ambiguities in inferring the identifies of sample proteins in the presence of shared peptides. Commonly used methods for computing protein-level confidence scores are discussed in detail. The review concludes with a discussion of several outstanding computational issues.
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44
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McIlwain S, Draghicescu P, Singh P, Goodlett DR, Noble WS. Detecting cross-linked peptides by searching against a database of cross-linked peptide pairs. J Proteome Res 2010; 9:2488-95. [PMID: 20349954 DOI: 10.1021/pr901163d] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mass spectrometric identification of cross-linked peptides can provide valuable information about the structure of protein complexes. We describe a straightforward database search scheme that identifies and assigns statistical confidence estimates to spectra from cross-linked peptides. The method is well suited to targeted analysis of a single protein complex, without requiring an isotope labeling strategy. Our approach uses a SEQUEST-style search procedure in which the database is comprised of a mixture of single peptides with and without linkers attached and cross-linked products. In contrast to several previous approaches, we generate theoretical spectra that account for all of the expected peaks from a cross-linked product, and we employ an empirical curve-fitting procedure to estimate statistical confidence measures. We show that our fully automated procedure successfully reidentifies spectra from a previous study, and we provide evidence that our statistical confidence estimates are accurate.
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Affiliation(s)
- Sean McIlwain
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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45
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Park CY, Klammer AA, Käll L, MacCoss MJ, Noble WS. Rapid and accurate peptide identification from tandem mass spectra. J Proteome Res 2008; 7:3022-7. [PMID: 18505281 DOI: 10.1021/pr800127y] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mass spectrometry, the core technology in the field of proteomics, promises to enable scientists to identify and quantify the entire complement of proteins in a complex biological sample. Currently, the primary bottleneck in this type of experiment is computational. Existing algorithms for interpreting mass spectra are slow and fail to identify a large proportion of the given spectra. We describe a database search program called Crux that reimplements and extends the widely used database search program Sequest. For speed, Crux uses a peptide indexing scheme to rapidly retrieve candidate peptides for a given spectrum. For each peptide in the target database, Crux generates shuffled decoy peptides on the fly, providing a good null model and, hence, accurate false discovery rate estimates. Crux also implements two recently described postprocessing methods: a p value calculation based upon fitting a Weibull distribution to the observed scores, and a semisupervised method that learns to discriminate between target and decoy matches. Both methods significantly improve the overall rate of peptide identification. Crux is implemented in C and is distributed with source code freely to noncommercial users.
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Affiliation(s)
- Christopher Y Park
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
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