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Lin A, Short T, Noble WS, Keich U. Improving Peptide-Level Mass Spectrometry Analysis via Double Competition. J Proteome Res 2022; 21:2412-2420. [PMID: 36166314 PMCID: PMC10108709 DOI: 10.1021/acs.jproteome.2c00282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The analysis of shotgun proteomics data often involves generating lists of inferred peptide-spectrum matches (PSMs) and/or of peptides. The canonical approach for generating these discovery lists is by controlling the false discovery rate (FDR), most commonly through target-decoy competition (TDC). At the PSM level, TDC is implemented by competing each spectrum's best-scoring target (real) peptide match with its best match against a decoy database. This PSM-level procedure can be adapted to the peptide level by selecting the top-scoring PSM per peptide prior to FDR estimation. Here, we first highlight and empirically augment a little known previous work by He et al., which showed that TDC-based PSM-level FDR estimates can be liberally biased. We thus propose that researchers instead focus on peptide-level analysis. We then investigate three ways to carry out peptide-level TDC and show that the most common method ("PSM-only") offers the lowest statistical power in practice. An alternative approach that carries out a double competition, first at the PSM and then at the peptide level ("PSM-and-peptide"), is the most powerful method, yielding an average increase of 17% more discovered peptides at 1% FDR threshold relative to the PSM-only method.
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Affiliation(s)
- Andy Lin
- Chemical and Biological Signatures, Pacific Northwest National Laboratory, Seattle, Washington 98109, United States
| | - Temana Short
- School of Mathematics & Statistics, University of Sydney, New South Wales, 2006, Australia
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Uri Keich
- School of Mathematics & Statistics, University of Sydney, New South Wales, 2006, Australia
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2
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Langford JB, Lurie IS. Use of micro, capillary, and nano liquid chromatography for forensic analysis. J Sep Sci 2021; 45:38-50. [PMID: 34626162 DOI: 10.1002/jssc.202100631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 01/03/2023]
Abstract
The use of micro, capillary, and nano liquid chromatography systems for forensic analysis has excellent potential. In a field where sample size is often limited, several studies have presented the viability of capillary columns with microflow and nanoflow, and when using mass spectrometric analysis limits of detection can be improved. Reduction in flow rates result in significant reduction in operating costs. Recent advances in miniaturized liquid chromatography systems also aim at in-laboratory and on-site detection, which have already been applied to forensic drug cases. This critical review will discuss the advantages, disadvantages, and applicability of microflow and nano liquid chromatography. In this regard, included in this article is a discussion of some promising areas not yet applied to forensic research.
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Affiliation(s)
- Joel B Langford
- Department of Forensic Science, The George Washington University, Washington, DC, 20007, USA
| | - Ira S Lurie
- Department of Forensic Science, The George Washington University, Washington, DC, 20007, USA
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3
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Lin A, Plubell DL, Keich U, Noble WS. Accurately Assigning Peptides to Spectra When Only a Subset of Peptides Are Relevant. J Proteome Res 2021; 20:4153-4164. [PMID: 34236864 PMCID: PMC8489664 DOI: 10.1021/acs.jproteome.1c00483] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The standard proteomics database search strategy involves searching spectra against a peptide database and estimating the false discovery rate (FDR) of the resulting set of peptide-spectrum matches. One assumption of this protocol is that all the peptides in the database are relevant to the hypothesis being investigated. However, in settings where researchers are interested in a subset of peptides, alternative search and FDR control strategies are needed. Recently, two methods were proposed to address this problem: subset-search and all-sub. We show that both methods fail to control the FDR. For subset-search, this failure is due to the presence of "neighbor" peptides, which are defined as irrelevant peptides with a similar precursor mass and fragmentation spectrum as a relevant peptide. Not considering neighbors compromises the FDR estimate because a spectrum generated by an irrelevant peptide can incorrectly match well to a relevant peptide. Therefore, we have developed a new method, "subset-neighbor search" (SNS), that accounts for neighbor peptides. We show evidence that SNS controls the FDR when neighbors are present and that SNS outperforms group-FDR, the only other method that appears to control the FDR relative to a subset of relevant peptides.
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Affiliation(s)
- Andy Lin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Deanna L. Plubell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Uri Keich
- School of Mathematics and Statistics, University of Sydney, NSW, Australia
| | - William S. Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School for Computer Science and Engineering, University of Washington, Seattle, WA, USA
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4
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O'Bryon I, Jenson SC, Merkley ED. Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification. Protein Sci 2020; 29:1864-1878. [PMID: 32713088 PMCID: PMC7454419 DOI: 10.1002/pro.3919] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022]
Abstract
Mass spectrometry-based proteomics is a popular and powerful method for precise and highly multiplexed protein identification. The most common method of analyzing untargeted proteomics data is called database searching, where the database is simply a collection of protein sequences from the target organism, derived from genome sequencing. Experimental peptide tandem mass spectra are compared to simplified models of theoretical spectra calculated from the translated genomic sequences. However, in several interesting application areas, such as forensics, archaeology, venomics, and others, a genome sequence may not be available, or the correct genome sequence to use is not known. In these cases, de novo peptide identification can play an important role. De novo methods infer peptide sequence directly from the tandem mass spectrum without reference to a sequence database, usually using graph-based or machine learning algorithms. In this review, we provide a basic overview of de novo peptide identification methods and applications, briefly covering de novo algorithms and tools, and focusing in more depth on recent applications from venomics, metaproteomics, forensics, and characterization of antibody drugs.
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Affiliation(s)
- Isabelle O'Bryon
- Chemical and Biological SignaturesPacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Sarah C. Jenson
- Chemical and Biological SignaturesPacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Eric D. Merkley
- Chemical and Biological SignaturesPacific Northwest National LaboratoryRichlandWashingtonUSA
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5
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Merkley ED, Burnum-Johnson KE, Anderson LN, Jenson SC, Wahl KL. Uniformly 15N-Labeled Recombinant Ricin A-Chain as an Internal Retention Time Standard for Increased Confidence in Forensic Identification of Ricin by Untargeted Nanoflow Liquid Chromatography-Tandem Mass Spectrometry. Anal Chem 2019; 91:13372-13376. [PMID: 31596564 DOI: 10.1021/acs.analchem.9b03389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ricin, a toxic protein from the castor plant, is of forensic and biosecurity interest because of its high toxicity and common occurrence in crimes and attempted crimes. Qualitative methods to detect ricin are therefore needed. Untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics methods are well suited because of their high specificity. Specificity in LC-MS/MS comes from both the LC and MS components. However, modern untargeted proteomics methods often use nanoflow LC, which has less reproducible retention times than standard-flow LC, making it challenging to use retention time as a point of identification in a forensic assay. We address this challenge by using retention times relative to a standard, namely, the uniformly 15N-labeled ricin A-chain produced recombinantly in a bacterial expression system. This material, added as an internal standard prior to trypsin digestion, produces a stable-isotope-labeled standard for every ricin tryptic peptide in the sample. We show that the MS signals for 15N and natural isotopic abundance ricin peptides are distinct, with mass shifts that correspond to the numbers of nitrogen atoms in each peptide or fragment. We also show that, as expected, labeled and unlabeled peptides coelute, with relative retention time differences of less than 0.2%.
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Affiliation(s)
- Eric D Merkley
- Chemical and Biological Signature Sciences Group , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Kristin E Burnum-Johnson
- Integrative Omics Group , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Lindsey N Anderson
- Biological Systems Science Group , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Sarah C Jenson
- Chemical and Biological Signature Sciences Group , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Karen L Wahl
- Integrative Omics Group , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
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6
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Heller NC, Garrett AM, Merkley ED, Cendrowski SR, Melville AM, Arce JS, Jenson SC, Wahl KL, Jarman KH. Probabilistic Limit of Detection for Ricin Identification Using a Shotgun Proteomics Assay. Anal Chem 2019; 91:12399-12406. [PMID: 31490662 DOI: 10.1021/acs.analchem.9b02721] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Robust and highly specific methods for the detection of the protein toxin ricin are of interest to the law enforcement community. In previous studies, methods based on liquid chromatography-tandem mass spectrometry shotgun proteomics have been proposed. The successful implementation of this approach relies on specific data evaluation criteria addressing (1) the quality of the mass spectrometric data, (2) the confidence of peptide identifications (peptide-spectrum matches), and (3) the number and sequence specificity of peptides detected. We present such data evaluation criteria and use a novel approach to establish the limit of detection for this ricin assay. Specifically, we use logistic regression to determine the probability of detection for individual ricin peptides at different concentrations. We then apply basic rules from probability theory, combining these individual peptide probabilities into an overall assay limit of detection. This procedure yields an assay limit of detection for ricin at 42.5 ng on column or 21.25 ng/μL for a 2-μL injection. We also show that, despite the conventional wisdom that detergents are deleterious to mass spectrometric analyses, the presence of Tween-20 did not prevent detection of ricin peptides, and indeed assays performed in buffers that included Tween-20 gave better results than assays performed using other buffer formulations with or without detergent removal.
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Affiliation(s)
| | - Alaine M Garrett
- National Biodefense Analysis and Countermeasures Center , Operated by BNBI for the U.S. Department of Homeland Security Science and Technology Directorate , Frederick , Maryland , United States
| | | | - Stephen R Cendrowski
- National Biodefense Analysis and Countermeasures Center , Operated by BNBI for the U.S. Department of Homeland Security Science and Technology Directorate , Frederick , Maryland , United States
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7
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O’Bryon I, Tucker AE, Kaiser BLD, Wahl KL, Merkley ED. Constructing a Tandem Mass Spectral Library for Forensic Ricin Identification. J Proteome Res 2019; 18:3926-3935. [DOI: 10.1021/acs.jproteome.9b00377] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Isabelle O’Bryon
- Chemical and Biological Signature Sciences Group, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Abigail E. Tucker
- Chemical and Biological Signature Sciences Group, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Brooke L. D. Kaiser
- Chemical and Biological Signature Sciences Group, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Karen L. Wahl
- Chemical and Biological Signature Sciences Group, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Eric D. Merkley
- Chemical and Biological Signature Sciences Group, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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8
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Applications and challenges of forensic proteomics. Forensic Sci Int 2019; 297:350-363. [DOI: 10.1016/j.forsciint.2019.01.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/09/2019] [Accepted: 01/13/2019] [Indexed: 12/23/2022]
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9
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Chen D, Bryden WA, Fenselau C. Rapid analysis of ricin using hot acid digestion and MALDI-TOF mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2018; 53:1013-1017. [PMID: 29974543 PMCID: PMC7278220 DOI: 10.1002/jms.4257] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/14/2018] [Accepted: 06/21/2018] [Indexed: 05/22/2023]
Abstract
Ricin is a protein toxin of considerable interest in forensics. A novel strategy is reported here for rapid detection of ricin based on microwave-assisted hot acid digestion and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry. Ricin samples are subjected to aspartate-selective hydrolysis, and biomarker peptide products are characterized by mass spectrometry. Spectra are obtained using post source decay and searched against a protein database. Several advantages are offered by chemical hydrolysis, relative to enzymatic hydrolysis, notably speed, robustness, and the production of heavier biomarkers. Agglutinin contamination is reliably recognized, as is the disulfide bond strongly characteristic of ricin.
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Affiliation(s)
- Dapeng Chen
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | | | - Catherine Fenselau
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
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Jarman KH, Heller NC, Jenson SC, Hutchison JR, Kaiser BLD, Payne SH, Wunschel DS, Merkley ED. Proteomics Goes to Court: A Statistical Foundation for Forensic Toxin/Organism Identification Using Bottom-Up Proteomics. J Proteome Res 2018; 17:3075-3085. [DOI: 10.1021/acs.jproteome.8b00212] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Kristin H. Jarman
- Applied Statistics and Computational Modeling Group, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Natalie C. Heller
- Applied Statistics and Computational Modeling Group, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Sarah C. Jenson
- Chemical and Biological Signatures Group, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Janine R. Hutchison
- Chemical and Biological Signatures Group, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Brooke L. Deatherage Kaiser
- Chemical and Biological Signatures Group, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Samuel H. Payne
- Biological Sciences Division, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - David S. Wunschel
- Chemical and Biological Signatures Group, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Eric D. Merkley
- Chemical and Biological Signatures Group, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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