1
|
Shannon AE, Teodorescu RN, Soon N, Heil LR, Jacob CC, Remes PM, Rubinstein MP, Searle BC. A workflow for targeted proteomics assay development using a versatile linear ion trap. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596891. [PMID: 38853838 PMCID: PMC11160733 DOI: 10.1101/2024.05.31.596891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Advances in proteomics and mass spectrometry have enabled the study of limited cell populations, such as single-cell proteomics, where high-mass accuracy instruments are typically required. While triple quadrupoles offer fast and sensitive nominal resolution measurements, these instruments are effectively limited to targeted proteomics. Linear ion traps (LITs) offer a versatile, cost-effective alternative capable of both targeted and global proteomics. We demonstrate a workflow using a newly released, hybrid quadrupole-LIT instrument for developing targeted proteomics assays from global data-independent acquisition (DIA) measurements without needing high-mass accuracy. Gas-phase fraction-based DIA enables rapid target library generation in the same background chemical matrix as each quantitative injection. Using a new software tool embedded within EncyclopeDIA for scheduling parallel reaction monitoring assays, we show consistent quantification across three orders of magnitude of input material. Using this approach, we demonstrate measuring peptide quantitative linearity down to 25x dilution in a background of only a 1 ng proteome without requiring stable isotope labeled standards. At 1 ng total protein on column, we found clear consistency between immune cell populations measured using flow cytometry and immune markers measured using LIT-based proteomics. We believe hybrid quadrupole-LIT instruments represent an economic solution to democratizing mass spectrometry in a wide variety of laboratory settings.
Collapse
|
2
|
Park J, Son A, Kim H. A protein-protein interaction analysis tool for targeted cross-linking mass spectrometry. Sci Rep 2023; 13:22103. [PMID: 38092875 PMCID: PMC10719354 DOI: 10.1038/s41598-023-49663-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023] Open
Abstract
Protein networking is critical to understanding the biological functions of proteins and the underlying mechanisms of disease. However, identifying physical protein-protein interactions (PPIs) can be challenging. To gain insights into target proteins that interact with a particular disease, we need to profile all the proteins involved in the disease beforehand. Although the cross-linking mass spectrometry (XL-MS) method is a representative approach to identify physical interactions between proteins, calculating theoretical mass values for application to targeted mass spectrometry can be difficult. To address this challenge, our research team developed PPIAT, a web application that integrates information on reviewed human proteins, protein-protein interactions, cross-linkers, enzymes, and modifications. PPIAT leverages publicly accessible databases such as STRING to identify interactomes associated with target proteins. Moreover, it autonomously computes the theoretical mass value, accounting for all potential cross-linking scenarios pertinent to the application of XL-MS in SRM analysis. The outputs generated by PPIAT can be concisely represented in terms of protein interaction probabilities, complemented by findings from alternative analytical tools like Prego. These comprehensive summaries enable researchers to customize the results according to specific experimental conditions. All functions of PPIAT are available for free on the web application, making it a valuable tool for researchers studying protein-protein interactions.
Collapse
Affiliation(s)
- Jongham Park
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Ahrum Son
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, 92037, USA
| | - Hyunsoo Kim
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea.
- Department of Convergent Bioscience and Informatics, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea.
- SCICS, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea.
| |
Collapse
|
3
|
Ebhardt HA, Ponchon P, Theodosiadis K, Fuerer C, Courtet-Compondu MC, O'Regan J, Affolter M, Joubran Y. Reduction of multiple reaction monitoring protein target list using correlation analysis. J Dairy Sci 2022; 105:7216-7229. [PMID: 35879160 DOI: 10.3168/jds.2021-21647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/15/2022] [Indexed: 11/19/2022]
Abstract
High mass resolution mass spectrometry provides hundreds to thousands of protein identifications per sample, and quantification is typically performed using label-free quantification. However, the gold standard of quantitative proteomics is multiple reaction monitoring (MRM) using triple quadrupole mass spectrometers and stable isotope reference peptides. This raises the question how to reduce a large data set to a small one without losing essential information. Here we present the reduction of such a data set using correlation analysis of bovine dairy ingredients and derived products. We were able to explain the variance in the proteomics data set using only 9 proteins across all major dairy protein classes: caseins, whey, and milk fat globule membrane proteins. We term this method Trinity-MRM. The reproducibility of the protein extraction and Trinity-MRM methods was shown to be below 5% in independent experiments (multi-day single-user and single-day multi-user) using double cream. Further application of this reductionist approach might include screening of large sample cohorts for biologically interesting samples before analysis by high-resolution mass spectrometry or other omics methodologies.
Collapse
Affiliation(s)
- Holger A Ebhardt
- Nestlé Development Centre Nutrition, Askeaton, County Limerick, Ireland, V94 E7P9
| | - Pierre Ponchon
- Nestlé Development Centre Nutrition, Askeaton, County Limerick, Ireland, V94 E7P9
| | | | - Christophe Fuerer
- Société des Produits Nestlé, Nestlé Research, Route du Jorat 57, 1000 Lausanne 26, Switzerland
| | | | - Jonathan O'Regan
- Nestlé Development Centre Nutrition, Askeaton, County Limerick, Ireland, V94 E7P9
| | - Michael Affolter
- Société des Produits Nestlé, Nestlé Research, Route du Jorat 57, 1000 Lausanne 26, Switzerland
| | - Yousef Joubran
- Nestlé Development Centre Nutrition, Askeaton, County Limerick, Ireland, V94 E7P9.
| |
Collapse
|
4
|
Abril AG, Carrera M, Notario V, Sánchez-Pérez Á, Villa TG. The Use of Bacteriophages in Biotechnology and Recent Insights into Proteomics. Antibiotics (Basel) 2022; 11:653. [PMID: 35625297 PMCID: PMC9137636 DOI: 10.3390/antibiotics11050653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 12/10/2022] Open
Abstract
Phages have certain features, such as their ability to form protein-protein interactions, that make them good candidates for use in a variety of beneficial applications, such as in human or animal health, industry, food science, food safety, and agriculture. It is essential to identify and characterize the proteins produced by particular phages in order to use these viruses in a variety of functional processes, such as bacterial detection, as vehicles for drug delivery, in vaccine development, and to combat multidrug resistant bacterial infections. Furthermore, phages can also play a major role in the design of a variety of cheap and stable sensors as well as in diagnostic assays that can either specifically identify specific compounds or detect bacteria. This article reviews recently developed phage-based techniques, such as the use of recombinant tempered phages, phage display and phage amplification-based detection. It also encompasses the application of phages as capture elements, biosensors and bioreceptors, with a special emphasis on novel bacteriophage-based mass spectrometry (MS) applications.
Collapse
Affiliation(s)
- Ana G. Abril
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain;
- Department of Food Technology, Spanish National Research Council (CSIC), Marine Research Institute (IIM), 36208 Vigo, Spain;
| | - Mónica Carrera
- Department of Food Technology, Spanish National Research Council (CSIC), Marine Research Institute (IIM), 36208 Vigo, Spain;
| | - Vicente Notario
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA;
| | - Ángeles Sánchez-Pérez
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW 2006, Australia;
| | - Tomás G. Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain;
| |
Collapse
|
5
|
Song J, Yu C. Alpha-Tri: a deep neural network for scoring the similarity between predicted and measured spectra improves peptide identification of DIA data. Bioinformatics 2022; 38:1525-1531. [PMID: 34999750 DOI: 10.1093/bioinformatics/btab878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 12/24/2021] [Accepted: 01/03/2022] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Peptide identification of data-independent acquisition (DIA) mass spectrometry applying the peptide-centric approach heavily relies on the spectral library matching, such as the fragment intensity similarity. If the intensity similarity is calculated through all possible fragment ions of a targeted peptide instead of just a few fragment ions provided by the spectral library, the matching will be more comprehensive and reliable, and thus the identification will be more confident. In addition, the emergence of high precision spectrum predictors, like Prosit, also makes it possible to capitalize on the predicted spectrum, which contains all possible fragment ion intensities, to calculate the intensity similarity for DIA data. RESULTS In this work, we propose Alpha-Tri, a neural-network-based model to calculate intensity similarity as a post-processing score using the predicted spectrum, measured spectrum and correlation spectrum (triple-spectrum). The predicted spectrum is generated by Prosit, the measured spectrum is retrieved from the apex of the chromatograms of all possible fragment ions and the correlation spectrum is used to indicate the present probabilities of these fragment ions as the link between the precursor and its fragment ions is lost in DIA. By adopting a data-driven method, Alpha-Tri is able to learn the intensity similarity from the triple-spectrum. This learned value is appended to initial scores from DIA-NN, allowing the ensuing statistical validation tool to report more peptides at the same false discovery rate (FDR). In our evaluation of the HeLa dataset with gradient lengths ranging from 0.5 to 2 h, Alpha-Tri delivered 3.0-7.2% gains in peptide detections at 1% FDR. On LFQbench dataset, a mixed-species dataset with known ratios, Alpha-Tri identified more peptides and proteins fell within the valid ratio ranges by up to 8.6% and 7.6%, respectively, compared with DIA-NN solely. AVAILABILITY AND IMPLEMENTATION The original datasets for benchmarks are downloaded from the ProteomeXchange with the identifiers PXD005573, PXD000954 and PXD002952. Source code is available at https://github.com/YuAirLab/Alpha-Tri.
Collapse
Affiliation(s)
- Jian Song
- Zhejiang University, Hangzhou, Zhejiang Province, China.,School of Engineering, Westlake University, Hangzhou, Zhejiang Province 310024, China.,Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250000, China
| | - Changbin Yu
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250000, China
| |
Collapse
|
6
|
Shanthamoorthy P, Young A, Röst H. Analyzing Assay Specificity in Metabolomics Using Unique Ion Signature Simulations. Anal Chem 2021; 93:11415-11423. [PMID: 34375078 DOI: 10.1021/acs.analchem.1c01204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Targeted, untargeted, and data-independent acquisition (DIA) metabolomics workflows are often hampered by ambiguous identification based on either MS1 information alone or relatively few MS2 fragment ions. While DIA methods have been popularized in proteomics, it is less clear whether they are suitable for metabolomics workflows due to their large precursor isolation windows and complex coisolation patterns. Here, we quantitatively investigate the conditions necessary for unique metabolite detection in complex backgrounds using precursor and fragment ion mass-to-charge (m/z) separation, comparing three benchmarked mass spectrometry (MS) methods [MS1, MRM (multiple reaction monitoring), and DIA]. Our simulations show that DIA outperformed MS1-only and MRM-based methods with regards to specificity by factors of ∼2.8-fold and ∼1.8-fold, respectively. Additionally, we show that our results are not dependent on the number of transitions used or the complexity of the background matrix. Finally, we show that collision energy is an important factor in unambiguous detection and that a single collision energy setting per compound cannot achieve optimal pairwise differentiation of compounds. Our analysis demonstrates the power of using both high-resolution precursor and high-resolution fragment ion m/z for unambiguous compound detection. This work also establishes DIA as an emerging MS acquisition method with high selectivity for metabolomics, outperforming both data-dependent acquisition (DDA) and MRM with regards to unique compound identification potential.
Collapse
Affiliation(s)
- Premy Shanthamoorthy
- Terrence Donnelly Centre for Cellular Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Adamo Young
- Terrence Donnelly Centre for Cellular Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Department of Computer Science, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Hannes Röst
- Terrence Donnelly Centre for Cellular Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Department of Computer Science, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| |
Collapse
|
7
|
Nakayasu ES, Gritsenko M, Piehowski PD, Gao Y, Orton DJ, Schepmoes AA, Fillmore TL, Frohnert BI, Rewers M, Krischer JP, Ansong C, Suchy-Dicey AM, Evans-Molina C, Qian WJ, Webb-Robertson BJM, Metz TO. Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation. Nat Protoc 2021; 16:3737-3760. [PMID: 34244696 PMCID: PMC8830262 DOI: 10.1038/s41596-021-00566-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 04/26/2021] [Indexed: 02/06/2023]
Abstract
Mass-spectrometry-based proteomic analysis is a powerful approach for discovering new disease biomarkers. However, certain critical steps of study design such as cohort selection, evaluation of statistical power, sample blinding and randomization, and sample/data quality control are often neglected or underappreciated during experimental design and execution. This tutorial discusses important steps for designing and implementing a liquid-chromatography-mass-spectrometry-based biomarker discovery study. We describe the rationale, considerations and possible failures in each step of such studies, including experimental design, sample collection and processing, and data collection. We also provide guidance for major steps of data processing and final statistical analysis for meaningful biological interpretations along with highlights of several successful biomarker studies. The provided guidelines from study design to implementation to data interpretation serve as a reference for improving rigor and reproducibility of biomarker development studies.
Collapse
Affiliation(s)
- Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Marina Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Paul D Piehowski
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Daniel J Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Athena A Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Thomas L Fillmore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Brigitte I Frohnert
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Marian Rewers
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Jeffrey P Krischer
- Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Charles Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Astrid M Suchy-Dicey
- Elson S. Floyd College of Medicine, Washington State University, Seattle, WA, USA
| | - Carmella Evans-Molina
- Center for Diabetes and Metabolic Diseases and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bobbie-Jo M Webb-Robertson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| |
Collapse
|
8
|
Wilburn DB, Richards AL, Swaney DL, Searle BC. CIDer: A Statistical Framework for Interpreting Differences in CID and HCD Fragmentation. J Proteome Res 2021; 20:1951-1965. [PMID: 33729787 DOI: 10.1021/acs.jproteome.0c00964] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Library searching is a powerful technique for detecting peptides using either data independent or data dependent acquisition. While both large-scale spectrum library curators and deep learning prediction approaches have focused on beam-type CID fragmentation (HCD), resonance CID fragmentation remains a popular technique. Here we demonstrate an approach to model the differences between HCD and CID spectra, and present a software tool, CIDer, for converting libraries between the two fragmentation methods. We demonstrate that just using a combination of simple linear models and basic principles of peptide fragmentation, we can explain up to 43% of the variation between ions fragmented by HCD and CID across an array of collision energy settings. We further show that in some circumstances, searching converted CID libraries can detect more peptides than searching existing CID libraries or libraries of machine learning predictions from FASTA databases. These results suggest that leveraging information in existing libraries by converting between HCD and CID libraries may be an effective interim solution while large-scale CID libraries are being developed.
Collapse
Affiliation(s)
- Damien B Wilburn
- Institute for Systems Biology, Seattle, Washington 98109, United States.,Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Alicia L Richards
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California 94158, United States.,J. David Gladstone Institutes, San Francisco, California 94158, United States.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| | - Danielle L Swaney
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California 94158, United States.,J. David Gladstone Institutes, San Francisco, California 94158, United States.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| | - Brian C Searle
- Institute for Systems Biology, Seattle, Washington 98109, United States
| |
Collapse
|
9
|
Vaca Jacome AS, Peckner R, Shulman N, Krug K, DeRuff KC, Officer A, Christianson KE, MacLean B, MacCoss MJ, Carr SA, Jaffe JD. Avant-garde: an automated data-driven DIA data curation tool. Nat Methods 2020; 17:1237-1244. [PMID: 33199889 PMCID: PMC7723322 DOI: 10.1038/s41592-020-00986-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 09/25/2020] [Indexed: 12/03/2022]
Abstract
Several challenges remain in data-independent acquisition (DIA) data analysis, such as to confidently identify peptides, define integration boundaries, remove interferences, and control false discovery rates. In practice, a visual inspection of the signals is still required, which is impractical with large datasets. We present Avant-garde as a tool to refine DIA (and parallel reaction monitoring) data. Avant-garde uses a novel data-driven scoring strategy: signals are refined by learning from the dataset itself, using all measurements in all samples to achieve the best optimization. We evaluate the performance of Avant-garde using benchmark DIA datasets and show that it can determine the quantitative suitability of a peptide peak, and reach the same levels of selectivity, accuracy, and reproducibility as manual validation. Avant-garde is complementary to existing DIA analysis engines and aims to establish a strong foundation for subsequent analysis of quantitative mass spectrometry data.
Collapse
Affiliation(s)
| | - Ryan Peckner
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cogen Therapeutics, Cambridge, MA, USA
| | | | - Karsten Krug
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Adam Officer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jacob D Jaffe
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Inzen Therapeutics, Cambridge, MA, USA.
- Inzen Therapeutics, Cambridge, MA, USA.
| |
Collapse
|
10
|
Carrera M, Pazos M, Gasset M. Proteomics-Based Methodologies for the Detection and Quantification of Seafood Allergens. Foods 2020; 9:foods9081134. [PMID: 32824679 PMCID: PMC7465946 DOI: 10.3390/foods9081134] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 12/18/2022] Open
Abstract
Seafood is considered one of the main food allergen sources by the European Food Safety Authority (EFSA). It comprises several distinct groups of edible aquatic animals, including fish and shellfish, such as crustacean and mollusks. Recently, the EFSA recognized the high risk of food allergy over the world and established the necessity of developing new methodologies for its control. Consequently, accurate, sensitive, and fast detection methods for seafood allergy control and detection in food products are highly recommended. In this work, we present a comprehensive review of the applications of the proteomics methodologies for the detection and quantification of seafood allergens. For this purpose, two consecutive proteomics strategies (discovery and targeted proteomics) that are applied to the study and control of seafood allergies are reviewed in detail. In addition, future directions and new perspectives are also provided.
Collapse
Affiliation(s)
- Mónica Carrera
- Institute of Marine Research (IIM), Spanish National Research Council (CSIC), 36208 Vigo, Spain; (M.C.); (M.P.)
| | - Manuel Pazos
- Institute of Marine Research (IIM), Spanish National Research Council (CSIC), 36208 Vigo, Spain; (M.C.); (M.P.)
| | - María Gasset
- Institute of Physical Chemistry Rocasolano (IQFR), Spanish National Research Council (CSIC), 28006 Madrid, Spain
- Correspondence: ; Tel.: +34-917-459-530
| |
Collapse
|
11
|
Carrera M, Piñeiro C, Martinez I. Proteomic Strategies to Evaluate the Impact of Farming Conditions on Food Quality and Safety in Aquaculture Products. Foods 2020; 9:E1050. [PMID: 32759674 PMCID: PMC7466198 DOI: 10.3390/foods9081050] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 02/08/2023] Open
Abstract
This review presents the primary applications of various proteomic strategies to evaluate the impact of farming conditions on food quality and safety in aquaculture products. Aquaculture is a quickly growing sector that represents 47% of total fish production. Food quality, dietary management, fish welfare, the stress response, food safety, and antibiotic resistance, which are covered by this review, are among the primary topics in which proteomic techniques and strategies are being successfully applied. The review concludes by outlining future directions and potential perspectives.
Collapse
Affiliation(s)
- Mónica Carrera
- Food Technology Department, Institute of Marine Research (IIM), Spanish National Research Council (CSIC), 36208 Vigo, Pontevedra, Spain
| | - Carmen Piñeiro
- Scientific Instrumentation and Quality Service (SICIM), Institute of Marine Research (IIM), Spanish National Research Council (CSIC), 36208 Vigo, Pontevedra, Spain;
| | - Iciar Martinez
- Research Centre for Experimental Marine Biology and Biotechnology—Plentzia Marine Station (PiE), University of the Basque Country UPV/EHU, 48620 Plentzia, Spain;
- IKERBASQUE Basque Foundation for Science, 48013 Bilbao, Spain
| |
Collapse
|
12
|
Pino LK, Searle BC, Bollinger JG, Nunn B, MacLean B, MacCoss MJ. The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics. MASS SPECTROMETRY REVIEWS 2020; 39:229-244. [PMID: 28691345 PMCID: PMC5799042 DOI: 10.1002/mas.21540] [Citation(s) in RCA: 390] [Impact Index Per Article: 97.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 06/01/2017] [Indexed: 05/03/2023]
Abstract
Skyline is a freely available, open-source Windows client application for accelerating targeted proteomics experimentation, with an emphasis on the proteomics and mass spectrometry community as users and as contributors. This review covers the informatics encompassed by the Skyline ecosystem, from computationally assisted targeted mass spectrometry method development, to raw acquisition file data processing, and quantitative analysis and results sharing.
Collapse
Affiliation(s)
- Lindsay K Pino
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Brian C Searle
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - James G Bollinger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Brook Nunn
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Brendan MacLean
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| |
Collapse
|
13
|
Krueger A, Stoll T, Shah AK, Sinha R, Frazer IH, Hill MM. Antibody-Free Multiplex Measurement of 23 Human Cytokines in Primary Cell Culture Secretome Using Targeted Mass Spectrometry. Anal Chem 2020; 92:3742-3750. [DOI: 10.1021/acs.analchem.9b05028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Annika Krueger
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - Thomas Stoll
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, Queensland 4006, Australia
| | - Alok K. Shah
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, Queensland 4006, Australia
| | - Rohit Sinha
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - Ian H. Frazer
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - Michelle M. Hill
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Brisbane, Queensland 4102, Australia
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, Queensland 4006, Australia
| |
Collapse
|
14
|
Mustafa S, Mobashir M. LC–MS and docking profiling reveals potential difference between the pure and crude fucoidan metabolites. Int J Biol Macromol 2020; 143:11-29. [DOI: 10.1016/j.ijbiomac.2019.11.232] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 11/24/2019] [Accepted: 11/29/2019] [Indexed: 12/19/2022]
|
15
|
Abstract
Metaproteomics can provide critical information about biological systems, but peptides are found within a complex background of other peptides. This complex background can change across samples, in some cases drastically. Cofragmentation, the coelution of peptides with similar mass to charge ratios, is one factor that influences which peptides are identified in an LC-MS/MS experiment: it is dependent on the nature and complexity of this dynamic background. Metaproteomics applications are particularly susceptible to cofragmentation-induced bias; they have vast protein sequence diversity and the abundance of those proteins can span many orders of magnitude. We have developed a mechanistic model that determines the number of potentially cofragmenting peptides in a given sample (called cobia, https://github.com/bertrand-lab/cobia ). We then used previously published data sets to validate our model, showing that the resulting peptide-specific score reflects the cofragmentation "risk" of peptides. Using an Antarctic sea ice edge metatranscriptome case study, we found that more rare taxonomic and functional groups are associated with higher cofragmentation bias. We also demonstrate how cofragmentation scores can be used to guide the selection of protein- or peptide-based biomarkers. We illustrate potential consequences of cofragmentation for multiple metaproteomic approaches, and suggest practical paths forward to cope with cofragmentation-induced bias.
Collapse
Affiliation(s)
- J Scott P McCain
- Department of Biology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada
| | - Erin M Bertrand
- Department of Biology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada
| |
Collapse
|
16
|
Application of immobilized ATP to the study of NLRP inflammasomes. Arch Biochem Biophys 2019; 670:104-115. [PMID: 30641048 DOI: 10.1016/j.abb.2018.12.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 12/01/2018] [Accepted: 12/17/2018] [Indexed: 01/15/2023]
Abstract
The NLRP proteins are a subfamily of the NOD-like receptor (NLR) innate immune sensors that possess an ATP-binding NACHT domain. As the most well studied member, NLRP3 can initiate the assembly process of a multiprotein complex, termed the inflammasome, upon detection of a wide range of microbial products and endogenous danger signals and results in the activation of pro-caspase-1, a cysteine protease that regulates multiple host defense pathways including cytokine maturation. Dysregulated NLRP3 activation contributes to inflammation and the pathogenesis of several chronic diseases, and the ATP-binding properties of NLRPs are thought to be critical for inflammasome activation. In light of this, we examined the utility of immobilized ATP matrices in the study of NLRP inflammasomes. Using NLRP3 as the prototypical member of the family, P-linked ATP Sepharose was determined to be a highly-effective capture agent. In subsequent examinations, P-linked ATP Sepharose was used as an enrichment tool to enable the effective profiling of NLRP3-biomarker signatures with selected reaction monitoring-mass spectrometry (SRM-MS). Finally, ATP Sepharose was used in combination with a fluorescence-linked enzyme chemoproteomic strategy (FLECS) screen to identify potential competitive inhibitors of NLRP3. The identification of a novel benzo[d]imidazol-2-one inhibitor that specifically targets the ATP-binding and hydrolysis properties of the NLRP3 protein implies that ATP Sepharose and FLECS could be applied other NLRPs as well.
Collapse
|
17
|
Deutsch EW, Perez-Riverol Y, Chalkley RJ, Wilhelm M, Tate S, Sachsenberg T, Walzer M, Käll L, Delanghe B, Böcker S, Schymanski EL, Wilmes P, Dorfer V, Kuster B, Volders PJ, Jehmlich N, Vissers JP, Wolan DW, Wang AY, Mendoza L, Shofstahl J, Dowsey AW, Griss J, Salek RM, Neumann S, Binz PA, Lam H, Vizcaíno JA, Bandeira N, Röst H. Expanding the Use of Spectral Libraries in Proteomics. J Proteome Res 2018; 17:4051-4060. [PMID: 30270626 PMCID: PMC6443480 DOI: 10.1021/acs.jproteome.8b00485] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The 2017 Dagstuhl Seminar on Computational Proteomics provided an opportunity for a broad discussion on the current state and future directions of the generation and use of peptide tandem mass spectrometry spectral libraries. Their use in proteomics is growing slowly, but there are multiple challenges in the field that must be addressed to further increase the adoption of spectral libraries and related techniques. The primary bottlenecks are the paucity of high quality and comprehensive libraries and the general difficulty of adopting spectral library searching into existing workflows. There are several existing spectral library formats, but none captures a satisfactory level of metadata; therefore, a logical next improvement is to design a more advanced, Proteomics Standards Initiative-approved spectral library format that can encode all of the desired metadata. The group discussed a series of metadata requirements organized into three designations of completeness or quality, tentatively dubbed bronze, silver, and gold. The metadata can be organized at four different levels of granularity: at the collection (library) level, at the individual entry (peptide ion) level, at the peak (fragment ion) level, and at the peak annotation level. Strategies for encoding mass modifications in a consistent manner and the requirement for encoding high-quality and commonly seen but as-yet-unidentified spectra were discussed. The group also discussed related topics, including strategies for comparing two spectra, techniques for generating representative spectra for a library, approaches for selection of optimal signature ions for targeted workflows, and issues surrounding the merging of two or more libraries into one. We present here a review of this field and the challenges that the community must address in order to accelerate the adoption of spectral libraries in routine analysis of proteomics datasets.
Collapse
Affiliation(s)
- Eric W. Deutsch
- Institute for Systems Biology, Seattle, Washington, 98109, United States
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Robert J. Chalkley
- University of California San Francisco, San Francisco, 94158, California, United States
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, 85354, Germany
| | | | - Timo Sachsenberg
- Department of Computer Science, Center for Bioinformatics, University of Tübingen, Sand 14, Tübingen, 72076, Germany
| | - Mathias Walzer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Lukas Käll
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH − Royal Institute of Technology, Stockholm 114 28, Sweden
| | - Bernard Delanghe
- Thermo Fisher Scientific Bremen, Hanna-Kunath Str. 11, 28199 Bremen, Germany
| | - Sebastian Böcker
- Chair for Bioinformatics, Friedrich-Schiller-University Jena, 07743 Jena, Germany
| | - Emma L. Schymanski
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Viktoria Dorfer
- University of Applied Sciences Upper Austria, Bioinformatics Research Group, Hagenberg, 4232, Austria
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, 85354, Germany
- Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich, Freising, 85354, Germany
| | | | - Nico Jehmlich
- Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | | | - Dennis W. Wolan
- Department of Molecular Medicine, The Scripps Research Institute, 92037, La Jolla, California, United States
| | - Ana Y. Wang
- Department of Molecular Medicine, The Scripps Research Institute, 92037, La Jolla, California, United States
| | - Luis Mendoza
- Institute for Systems Biology, Seattle, Washington, 98109, United States
| | - Jim Shofstahl
- Thermo Fisher Scientific, 355 River Oaks Parkway San Jose, CA 95134
| | - Andrew W. Dowsey
- Department of Population Health Sciences and Bristol Veterinary School, Faculty of Health Sciences, University of Bristol, Bristol BS9 1BN, UK
| | - Johannes Griss
- Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Währinger Gürtel 18-20, Vienna 1090, Austria
| | - Reza M. Salek
- The International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon CEDEX 08, France
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry, Department of Stress and Developmental Biology, 06120 Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Pierre-Alain Binz
- Clinical Chemistry Service, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
| | - Henry Lam
- Department of Chemical and Biological Engineering, the Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, Department of Computer Science and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 92093-0404, USA
| | - Hannes Röst
- The Donnelly Centre, University of Toronto, 160 College St., Toronto, ON, M5S 3E1, Canada
| |
Collapse
|
18
|
Tarasova IA, Masselon CD, Gorshkov AV, Gorshkov MV. Predictive chromatography of peptides and proteins as a complementary tool for proteomics. Analyst 2018; 141:4816-4832. [PMID: 27419248 DOI: 10.1039/c6an00919k] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In the last couple of decades, considerable effort has been focused on developing methods for quantitative and qualitative proteome characterization. The method of choice in this characterization is mass spectrometry used in combination with sample separation. One of the most widely used separation techniques at the front end of a mass spectrometer is high performance liquid chromatography (HPLC). A unique feature of HPLC is its specificity to the amino acid sequence of separated peptides and proteins. This specificity may provide additional information about the peptides or proteins under study which is complementary to the mass spectrometry data. The value of this information for proteomics has been recognized in the past few decades, which has stimulated significant effort in the development and implementation of computational and theoretical models for the prediction of peptide retention time for a given sequence. Here we review the advances in this area and the utility of predicted retention times for proteomic applications.
Collapse
Affiliation(s)
- Irina A Tarasova
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russia.
| | - Christophe D Masselon
- CEA, iRTSV-BGE, Laboratoire d'Etude de la Dynamique des Protéomes, Grenoble, F-38000, France and INSERM, U1038-BGE, F-38000, Grenoble, France
| | - Alexander V Gorshkov
- N.N. Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Mikhail V Gorshkov
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russia. and Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow region 141700, Russia
| |
Collapse
|
19
|
Ludwig C, Gillet L, Rosenberger G, Amon S, Collins BC, Aebersold R. Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial. Mol Syst Biol 2018; 14:e8126. [PMID: 30104418 PMCID: PMC6088389 DOI: 10.15252/msb.20178126] [Citation(s) in RCA: 578] [Impact Index Per Article: 96.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 05/11/2018] [Accepted: 05/15/2018] [Indexed: 01/16/2023] Open
Abstract
Many research questions in fields such as personalized medicine, drug screens or systems biology depend on obtaining consistent and quantitatively accurate proteomics data from many samples. SWATH-MS is a specific variant of data-independent acquisition (DIA) methods and is emerging as a technology that combines deep proteome coverage capabilities with quantitative consistency and accuracy. In a SWATH-MS measurement, all ionized peptides of a given sample that fall within a specified mass range are fragmented in a systematic and unbiased fashion using rather large precursor isolation windows. To analyse SWATH-MS data, a strategy based on peptide-centric scoring has been established, which typically requires prior knowledge about the chromatographic and mass spectrometric behaviour of peptides of interest in the form of spectral libraries and peptide query parameters. This tutorial provides guidelines on how to set up and plan a SWATH-MS experiment, how to perform the mass spectrometric measurement and how to analyse SWATH-MS data using peptide-centric scoring. Furthermore, concepts on how to improve SWATH-MS data acquisition, potential trade-offs of parameter settings and alternative data analysis strategies are discussed.
Collapse
Affiliation(s)
- Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany
| | - Ludovic Gillet
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - George Rosenberger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Sabine Amon
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
| |
Collapse
|
20
|
Ulke-Lemée A, Lau A, Nelson MC, James MT, Muruve DA, MacDonald JA. Quantification of Inflammasome Adaptor Protein ASC in Biological Samples by Multiple-Reaction Monitoring Mass Spectrometry. Inflammation 2018; 41:1396-1408. [DOI: 10.1007/s10753-018-0787-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
21
|
Doneanu C, Fang J, Alelyunas Y, Yu YQ, Wrona M, Chen W. An HS-MRM Assay for the Quantification of Host-cell Proteins in Protein Biopharmaceuticals by Liquid Chromatography Ion Mobility QTOF Mass Spectrometry. J Vis Exp 2018. [PMID: 29733313 PMCID: PMC6100639 DOI: 10.3791/55325] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The analysis of low-level (1-100 ppm) protein impurities (e.g., host-cell proteins (HCPs)) in protein biotherapeutics is a challenging assay requiring high sensitivity and a wide dynamic range. Mass spectrometry-based quantification assays for proteins typically involve protein digestion followed by the selective reaction monitoring/multiple reaction monitoring (SRM/MRM) quantification of peptides using a low-resolution (Rs ~1,000) tandem quadrupole mass spectrometer. One of the limitations of this approach is the interference phenomenon observed when the peptide of interest has the "same" precursor and fragment mass (in terms of m/z values) as other co-eluting peptides present in the sample (within a 1-Da window). To avoid this phenomenon, we propose an alternative mass spectrometric approach, a high selectivity (HS) MRM assay that combines the ion mobility separation of peptide precursors with the high-resolution (Rs ~30,000) MS detection of peptide fragments. We explored the capabilities of this approach to quantify low-abundance peptide standards spiked in a monoclonal antibody (mAb) digest and demonstrated that it has the sensitivity and dynamic range (at least 3 orders of magnitude) typically achieved in HCP analysis. All six peptide standards were detected at concentrations as low as 0.1 nM (1 femtomole loaded on a 2.1-mm ID chromatographic column) in the presence of a high-abundance peptide background (2 µg of a mAb digest loaded on-column). When considering the MW of rabbit phosphorylase (97.2 kDa), from which the spiked peptides were derived, the LOQ of this assay is lower than 50 ppm. Relative standard deviations (RSD) of peak areas (n = 4 replicates) were less than 15% across the entire concentration range investigated (0.1-100 nM or 1-1,000 ppm) in this study.
Collapse
|
22
|
Manual method of visually identifying candidate signals for a targeted peptide. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1083:258-270. [PMID: 29554522 DOI: 10.1016/j.jchromb.2018.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 01/05/2018] [Accepted: 01/15/2018] [Indexed: 11/20/2022]
Abstract
The purpose of this study is to improve peptide signal identification in groups of extracted ion chromatograms (XICs) obtained with the liquid chromatography-selected reaction monitoring (LC-SRM) technique and a triple quadrupole mass spectrometer (QqQ) operating in one of the supported multiple reaction monitoring (MRM) modes. The imperfection of quadrupole mass analyzers causes ion interference, which impedes the identification of peptide signals as chromatographic peak groups in relevant retention time intervals. To investigate this problem in depth, the QqQ conversion of the eluate into XIC groups was considered as the consecutive transformations of the particles' abundances as the corresponding functions of retention time. In this study, the hypothesis that, during this conversion, the same chromatographic profile should be preserved as an implicit sign in each chromatographic peak of the signal was confirmed for peptides. To examine chromatographic profiles, continuous transformations of XIC groups were derived and implemented in srm2prot Express software (s2pe, http://msr.ibmc.msk.ru/s2pe). Because of ion interference, several peptide-like signals may appear in one XIC group. Therefore, these signals must be considered candidates for a targeted peptide's signal and should be resolved after identification. The theoretical investigation of intensity functions as XICs that are not distorted by noise produced three rules for Identifying Candidate Signals for a targeted Peptide (ICSP, http://msr.ibmc.msk.ru/ICSP) that constitute the proposed manual visual method. We theoretically and experimentally compared this method with the conventional semiempirical intuitive technique and found that the former significantly streamlines peptide signal identification and avoids typical errors.
Collapse
|
23
|
Chappellaz M, Segboer H, Ulke-Lemée A, Sutherland C, Chen HM, MacDonald JA. Quantitation of myosin regulatory light chain phosphorylation in biological samples with multiple reaction monitoring mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:608-616. [PMID: 29567090 DOI: 10.1016/j.bbapap.2018.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 02/22/2018] [Accepted: 03/16/2018] [Indexed: 10/17/2022]
Abstract
The 20-kDa regulatory light chain of myosin II plays an important role in regulating smooth muscle contractile force. LC20 is phosphorylated canonically by myosin light chain kinase in a Ca2+/calmodulin-dependent manner at S19. The diphosphorylation of LC20 at T18 and S19 has been observed in smooth muscle tissues. Given that the phosphorylation of LC20 is positively correlated with tension development, the molar stoichiometry of LC20 phosphorylation is commonly profiled as a measure of smooth muscle contractility. Herein, we describe a novel multiple reaction monitoring (MRM)-mass spectrometry (MS) approach for the quantification of LC20 phosphorylation at T18 and S19. Unique precursor as well as y- and b-ion transitions were identified for unphosphorylated LC20-(TS), monophosphorylated LC20-(TpS) and diphosphorylated LC20-(pTpS) peptides. The MRM-MS assay could accurately define molar phosphorylation stoichiometries of S19 and T18 over a broad range (i.e., 0-2 mol P/mol LC20). Correlations of the results for two quantification techniques indicate that the MRM-MS assay performs equally to Phos-tag SDS-PAGE for the determination of LC20 phosphorylation stoichiometry in arterial tissue samples. The MRM-MS technique provides a robust alternative to antibody-based detection systems for the quantification of LC20 phosphorylation.
Collapse
Affiliation(s)
- Mona Chappellaz
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
| | - Hayden Segboer
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
| | - Annegret Ulke-Lemée
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
| | - Cindy Sutherland
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
| | - Huey-Miin Chen
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
| | - Justin A MacDonald
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada.
| |
Collapse
|
24
|
Manes NP, Nita-Lazar A. Application of targeted mass spectrometry in bottom-up proteomics for systems biology research. J Proteomics 2018; 189:75-90. [PMID: 29452276 DOI: 10.1016/j.jprot.2018.02.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/25/2018] [Accepted: 02/07/2018] [Indexed: 02/08/2023]
Abstract
The enormous diversity of proteoforms produces tremendous complexity within cellular proteomes, facilitates intricate networks of molecular interactions, and constitutes a formidable analytical challenge for biomedical researchers. Currently, quantitative whole-proteome profiling often relies on non-targeted liquid chromatography-mass spectrometry (LC-MS), which samples proteoforms broadly, but can suffer from lower accuracy, sensitivity, and reproducibility compared with targeted LC-MS. Recent advances in bottom-up proteomics using targeted LC-MS have enabled previously unachievable identification and quantification of target proteins and posttranslational modifications within complex samples. Consequently, targeted LC-MS is rapidly advancing biomedical research, especially systems biology research in diverse areas that include proteogenomics, interactomics, kinomics, and biological pathway modeling. With the recent development of targeted LC-MS assays for nearly the entire human proteome, targeted LC-MS is positioned to enable quantitative proteomic profiling of unprecedented quality and accessibility to support fundamental and clinical research. Here we review recent applications of bottom-up proteomics using targeted LC-MS for systems biology research. SIGNIFICANCE: Advances in targeted proteomics are rapidly advancing systems biology research. Recent applications include systems-level investigations focused on posttranslational modifications (such as phosphoproteomics), protein conformation, protein-protein interaction, kinomics, proteogenomics, and metabolic and signaling pathways. Notably, absolute quantification of metabolic and signaling pathway proteins has enabled accurate pathway modeling and engineering. Integration of targeted proteomics with other technologies, such as RNA-seq, has facilitated diverse research such as the identification of hundreds of "missing" human proteins (genes and transcripts that appear to encode proteins but direct experimental evidence was lacking).
Collapse
Affiliation(s)
- Nathan P Manes
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aleksandra Nita-Lazar
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
25
|
Clinical proteomics: Insights from IGF-I. Clin Chim Acta 2018; 477:18-23. [DOI: 10.1016/j.cca.2017.11.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/27/2017] [Accepted: 11/27/2017] [Indexed: 01/09/2023]
|
26
|
A review on mass spectrometry-based quantitative proteomics: Targeted and data independent acquisition. Anal Chim Acta 2017; 964:7-23. [DOI: 10.1016/j.aca.2017.01.059] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 01/03/2017] [Accepted: 01/05/2017] [Indexed: 01/18/2023]
|
27
|
Röst HL, Malmström L, Aebersold R. Reproducible quantitative proteotype data matrices for systems biology. Mol Biol Cell 2016; 26:3926-31. [PMID: 26543201 PMCID: PMC4710225 DOI: 10.1091/mbc.e15-07-0507] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Historically, many mass spectrometry–based proteomic studies have aimed at compiling an inventory of protein compounds present in a biological sample, with the long-term objective of creating a proteome map of a species. However, to answer fundamental questions about the behavior of biological systems at the protein level, accurate and unbiased quantitative data are required in addition to a list of all protein components. Fueled by advances in mass spectrometry, the proteomics field has thus recently shifted focus toward the reproducible quantification of proteins across a large number of biological samples. This provides the foundation to move away from pure enumeration of identified proteins toward quantitative matrices of many proteins measured across multiple samples. It is argued here that data matrices consisting of highly reproducible, quantitative, and unbiased proteomic measurements across a high number of conditions, referred to here as quantitative proteotype maps, will become the fundamental currency in the field and provide the starting point for downstream biological analysis. Such proteotype data matrices, for example, are generated by the measurement of large patient cohorts, time series, or multiple experimental perturbations. They are expected to have a large effect on systems biology and personalized medicine approaches that investigate the dynamic behavior of biological systems across multiple perturbations, time points, and individuals.
Collapse
Affiliation(s)
- Hannes L Röst
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, CH-8093 Zurich, Switzerland Department of Genetics, Stanford University, Stanford, CA 94305
| | - Lars Malmström
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, CH-8093 Zurich, Switzerland S3IT, University of Zurich, CH-8057 Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, CH-8093 Zurich, Switzerland Faculty of Science, University of Zurich, CH-8057 Zurich, Switzerland
| |
Collapse
|
28
|
Mesuere B, Van der Jeugt F, Devreese B, Vandamme P, Dawyndt P. The unique peptidome: Taxon-specific tryptic peptides as biomarkers for targeted metaproteomics. Proteomics 2016; 16:2313-8. [DOI: 10.1002/pmic.201600023] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 06/13/2016] [Accepted: 07/01/2016] [Indexed: 12/23/2022]
Affiliation(s)
- Bart Mesuere
- Department of Applied Mathematics; Computer Science and Statistics; Faculty of Sciences; Ghent University; Ghent Belgium
| | - Felix Van der Jeugt
- Department of Applied Mathematics; Computer Science and Statistics; Faculty of Sciences; Ghent University; Ghent Belgium
| | - Bart Devreese
- Laboratory for Protein Biochemistry and Biomolecular Engineering; Faculty of Sciences; Ghent University; Ghent Belgium
| | - Peter Vandamme
- Laboratory for Microbiology; Faculty of Sciences; Ghent University; Ghent Belgium
| | - Peter Dawyndt
- Department of Applied Mathematics; Computer Science and Statistics; Faculty of Sciences; Ghent University; Ghent Belgium
| |
Collapse
|
29
|
White FM, Wolf-Yadlin A. Methods for the Analysis of Protein Phosphorylation-Mediated Cellular Signaling Networks. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2016; 9:295-315. [PMID: 27049636 DOI: 10.1146/annurev-anchem-071015-041542] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Protein phosphorylation-mediated cellular signaling networks regulate almost all aspects of cell biology, including the responses to cellular stimulation and environmental alterations. These networks are highly complex and comprise hundreds of proteins and potentially thousands of phosphorylation sites. Multiple analytical methods have been developed over the past several decades to identify proteins and protein phosphorylation sites regulating cellular signaling, and to quantify the dynamic response of these sites to different cellular stimulation. Here we provide an overview of these methods, including the fundamental principles governing each method, their relative strengths and weaknesses, and some examples of how each method has been applied to the analysis of complex signaling networks. When applied correctly, each of these techniques can provide insight into the topology, dynamics, and regulation of protein phosphorylation signaling networks.
Collapse
Affiliation(s)
- Forest M White
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139;
| | | |
Collapse
|
30
|
Potts GK, Voigt EA, Bailey DJ, Rose CM, Westphall MS, Hebert AS, Yin J, Coon JJ. Neucode Labels for Multiplexed, Absolute Protein Quantification. Anal Chem 2016; 88:3295-303. [PMID: 26882330 PMCID: PMC5141612 DOI: 10.1021/acs.analchem.5b04773] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We describe a new method to accomplish multiplexed, absolute protein quantification in a targeted fashion. The approach draws upon the recently developed neutron encoding (NeuCode) metabolic labeling strategy and parallel reaction monitoring (PRM). Since PRM scanning relies upon high-resolution tandem mass spectra for targeted protein quantification, incorporation of multiple NeuCode labeled peptides permits high levels of multiplexing that can be accessed from high-resolution tandem mass spectra. Here we demonstrate this approach in cultured cells by monitoring a viral infection and the corresponding viral protein production over many infection time points in a single experiment. In this context the NeuCode PRM combination affords up to 30 channels of quantitative information in a single MS experiment.
Collapse
Affiliation(s)
- Gregory K Potts
- Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Emily A Voigt
- Department of Chemical and Biological Engineering, University of Wisconsin , Madison, Wisconsin 53706, United States
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Derek J Bailey
- Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Christopher M Rose
- Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Michael S Westphall
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Alexander S Hebert
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - John Yin
- Department of Chemical and Biological Engineering, University of Wisconsin , Madison, Wisconsin 53706, United States
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| |
Collapse
|
31
|
Abstract
The emerging field of proteomics has contributed greatly to improving our understanding of the human pathogen Mycobacterium tuberculosis over the last two decades. In this chapter we provide a comprehensive overview of mycobacterial proteome research and highlight key findings. First, studies employing a combination of two-dimensional gel electrophoresis and mass spectrometry (MS) provided insights into the proteomic composition, initially of the whole bacillus and subsequently of subfractions, such as the cell wall, cytosol, and secreted proteins. Comparison of results obtained under various culture conditions, i.e., acidic pH, nutrient starvation, and low oxygen tension, aiming to mimic facets of the intracellular lifestyle of M. tuberculosis, provided initial clues to proteins relevant for intracellular survival and manipulation of the host cell. Further attempts were aimed at identifying the biological functions of the hypothetical M. tuberculosis proteins, which still make up a quarter of the gene products of M. tuberculosis, and at characterizing posttranslational modifications. Recent technological advances in MS have given rise to new methods such as selected reaction monitoring (SRM) and data-independent acquisition (DIA). These targeted, cutting-edge techniques combined with a public database of specific MS assays covering the entire proteome of M. tuberculosis allow the simple and reliable detection of any mycobacterial protein. Most recent studies attempt not only to identify but also to quantify absolute amounts of single proteins in the complex background of host cells without prior sample fractionation or enrichment. Finally, we will discuss the potential of proteomics to advance vaccinology, drug discovery, and biomarker identification to improve intervention and prevention measures for tuberculosis.
Collapse
|
32
|
Percy AJ, Yang J, Chambers AG, Mohammed Y, Miliotis T, Borchers CH. Protocol for Standardizing High-to-Moderate Abundance Protein Biomarker Assessments Through an MRM-with-Standard-Peptides Quantitative Approach. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:515-530. [DOI: 10.1007/978-3-319-41448-5_24] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
33
|
McNulty SN, Rosa BA, Fischer PU, Rumsey JM, Erdmann-Gilmore P, Curtis KC, Specht S, Townsend RR, Weil GJ, Mitreva M. An Integrated Multiomics Approach to Identify Candidate Antigens for Serodiagnosis of Human Onchocerciasis. Mol Cell Proteomics 2015; 14:3224-33. [PMID: 26472727 PMCID: PMC4762623 DOI: 10.1074/mcp.m115.051953] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 09/10/2015] [Indexed: 11/27/2022] Open
Abstract
Improved diagnostic methods are needed to support ongoing efforts to eliminate onchocerciasis (river blindness). This study used an integrated approach to identify adult female Onchocerca volvulus antigens that can be explored for developing serodiagnostic tests. The first step was to develop a detailed multi-omics database of all O. volvulus proteins deduced from the genome, gene transcription data for different stages of the parasite including eight individual female worms (providing gene expression information for 94.8% of all protein coding genes), and the adult female worm proteome (detecting 2126 proteins). Next, female worm proteins were purified with IgG antibodies from onchocerciasis patients and identified using LC-MS with a high-resolution hybrid quadrupole-time-of-flight mass spectrometer. A total of 241 immunoreactive proteins were identified among those bound by IgG from infected individuals but not IgG from uninfected controls. These included most of the major diagnostic antigens described over the past 25 years plus many new candidates. Proteins of interest were prioritized for further study based on a lack of conservation with orthologs in the human host and other helminthes, their expression pattern across the life cycle, and their consistent expression among individual female worms. Based on these criteria, we selected 33 proteins that should be carried forward for testing as serodiagnostic antigens to supplement existing diagnostic tools. These candidates, together with the extensive pan-omics dataset generated in this study are available to the community (http://nematode.net) to facilitate basic and translational research on onchocerciasis.
Collapse
Affiliation(s)
- Samantha N McNulty
- From the ‡McDonnell Genome Institute, Washington University in St Louis, Missouri 63108
| | - Bruce A Rosa
- From the ‡McDonnell Genome Institute, Washington University in St Louis, Missouri 63108
| | - Peter U Fischer
- §Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Jeanne M Rumsey
- ¶Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Petra Erdmann-Gilmore
- ¶Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Kurt C Curtis
- §Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Sabine Specht
- **Institute for Medical Microbiology, Immunology and Parasitology, University Hospital of Bonn, Bonn, Germany 53127
| | - R Reid Townsend
- ¶Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110; ‖Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Gary J Weil
- §Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Makedonka Mitreva
- From the ‡McDonnell Genome Institute, Washington University in St Louis, Missouri 63108; §Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110;
| |
Collapse
|
34
|
Adeola HA, Calder B, Soares NC, Kaestner L, Blackburn JM, Zerbini LF. In silico verification and parallel reaction monitoring prevalidation of potential prostate cancer biomarkers. Future Oncol 2015; 12:43-57. [PMID: 26615920 DOI: 10.2217/fon.15.296] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
PURPOSE Targeted proteomics of potential biomarkers is often challenging. Hence, we developed an intermediate workflow to streamline potential urinary biomarkers of prostate cancer (PCa). MATERIALS & METHODS Using previously discovered potential PCa biomarkers; we selected proteotypic peptides for targeted validation. Preliminary in silico immunohistochemical and single reaction monitoring (SRM) verification was performed. Successful PTPs were then prevalidated using parallel reaction monitoring (PRM) and reconfirmed in 15 publicly available databases. RESULTS Stringency-based targetable potential biomarkers were shortlisted following in silico screening. PRM reveals top 12 potential biomarkers including the top ranking seven in silico verification-based biomarkers. Database reconfirmation showed differential expression between PCa and benign/normal prostatic urine samples. CONCLUSION The pragmatic penultimate screening step, described herein, would immensely improve targeted proteomics validation of potential disease biomarkers.
Collapse
Affiliation(s)
- Henry A Adeola
- International Centre for Genetic Engineering & Biotechnology, Cape Town, South Africa.,Institute of Infectious Diseases & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Bridget Calder
- Institute of Infectious Diseases & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Nelson C Soares
- Institute of Infectious Diseases & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Lisa Kaestner
- Urology Department, Grootes Schuur Hospital, Cape Town, South Africa
| | - Jonathan M Blackburn
- Institute of Infectious Diseases & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Luiz F Zerbini
- International Centre for Genetic Engineering & Biotechnology, Cape Town, South Africa.,Institute of Infectious Diseases & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| |
Collapse
|
35
|
Porter CJ, Bereman MS. Data-independent-acquisition mass spectrometry for identification of targeted-peptide site-specific modifications. Anal Bioanal Chem 2015; 407:6627-35. [PMID: 26105512 PMCID: PMC5257204 DOI: 10.1007/s00216-015-8819-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/17/2015] [Accepted: 06/01/2015] [Indexed: 12/22/2022]
Abstract
We present a novel strategy based on data-independent acquisition coupled to targeted data extraction for the detection and identification of site-specific modifications of targeted peptides in a completely unbiased manner. This method requires prior knowledge of the site of the modification along the peptide backbone from the protein of interest, but not the mass of the modification. The procedure, named multiplex adduct peptide profiling (MAPP), consists of three steps: 1) A fragment-ion tag is extracted from the data, consisting of the b-type and y-type ion series from the N and C-terminus, respectively, up to the amino-acid position that is believed to be modified; 2) MS1 features are matched to the fragment-ion tag in retention-time space, using the isolation window as a pre-filter to enable calculation of the mass of the modification; and 3) modified fragment ions are overlaid with the unmodified fragment ions to verify the mass calculated in step 2. We discuss the development, applications, and limitations of this new method for detection of unknown peptide modifications. We present an application of the method in profiling adducted peptides derived from abundant proteins in biological fluids with the ultimate objective of detecting biomarkers of exposure to reactive species.
Collapse
Affiliation(s)
- Caleb J Porter
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | | |
Collapse
|
36
|
Kitata RB, Dimayacyac-Esleta BRT, Choong WK, Tsai CF, Lin TD, Tsou CC, Weng SH, Chen YJ, Yang PC, Arco SD, Nesvizhskii AI, Sung TY, Chen YJ. Mining Missing Membrane Proteins by High-pH Reverse-Phase StageTip Fractionation and Multiple Reaction Monitoring Mass Spectrometry. J Proteome Res 2015. [PMID: 26202522 DOI: 10.1021/acs.jproteome.5b00477] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite significant efforts in the past decade toward complete mapping of the human proteome, 3564 proteins (neXtProt, 09-2014) are still "missing proteins". Over one-third of these missing proteins are annotated as membrane proteins, owing to their relatively challenging accessibility with standard shotgun proteomics. Using nonsmall cell lung cancer (NSCLC) as a model study, we aim to mine missing proteins from disease-associated membrane proteome, which may be still largely under-represented. To increase identification coverage, we employed Hp-RP StageTip prefractionation of membrane-enriched samples from 11 NSCLC cell lines. Analysis of membrane samples from 20 pairs of tumor and adjacent normal lung tissue was incorporated to include physiologically expressed membrane proteins. Using multiple search engines (X!Tandem, Comet, and Mascot) and stringent evaluation of FDR (MAYU and PeptideShaker), we identified 7702 proteins (66% membrane proteins) and 178 missing proteins (74 membrane proteins) with PSM-, peptide-, and protein-level FDR of 1%. Through multiple reaction monitoring using synthetic peptides, we provided additional evidence of eight missing proteins including seven with transmembrane helix domains. This study demonstrates that mining missing proteins focused on cancer membrane subproteome can greatly contribute to map the whole human proteome. All data were deposited into ProteomeXchange with the identifier PXD002224.
Collapse
Affiliation(s)
- Reta Birhanu Kitata
- Institute of Chemistry, Academia Sinica , No. 128, Academia Road Sec. 2, Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University , 101, Sec 2, Kuang-Fu Road, Hsinchu 30013, Taiwan.,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica , No. 1, Roosevelt Road, Sec. 4, Taipei 10617, Taiwan
| | - Baby Rorielyn T Dimayacyac-Esleta
- Institute of Chemistry, Academia Sinica , No. 128, Academia Road Sec. 2, Taipei 115, Taiwan.,Institute of Chemistry, University of the Philippines , Diliman Quezon City, Philippines
| | - Wai-Kok Choong
- Institute of Information Science, Academia Sinica , 128 Academia Road, Section 2, Taipei 115, Taiwan
| | - Chia-Feng Tsai
- Institute of Chemistry, Academia Sinica , No. 128, Academia Road Sec. 2, Taipei 115, Taiwan
| | - Tai-Du Lin
- Institute of Chemistry, Academia Sinica , No. 128, Academia Road Sec. 2, Taipei 115, Taiwan.,Department of Biochemical Sciences, National Taiwan University , 1 Roosevelt Road, Sec. 4, Taipei 106, Taiwan
| | - Chih-Chiang Tsou
- Department of Computational Medicine and Bioinformatics and Department of Pathology, University of Michigan Medical School , 1301 Catherine, Ann Arbor, Michigan 48109, United States
| | - Shao-Hsing Weng
- Institute of Chemistry, Academia Sinica , No. 128, Academia Road Sec. 2, Taipei 115, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University , 1, Roosevelt Road, Section 4, Taipei 10617, Taiwan
| | - Yi-Ju Chen
- Institute of Chemistry, Academia Sinica , No. 128, Academia Road Sec. 2, Taipei 115, Taiwan
| | - Pan-Chyr Yang
- Department of Internal Medicine, National Taiwan University Hospital , 1 Jen-Ai Road, Section 1, Taipei 10051, Taiwan.,National Taiwan University College of Medicine , No. 1, Section 1, Ren'ai Road, Taipei 100, Taiwan.,Institute of Biomedical Science, Academia Sinica , 128 Academia Road, Section 2, Taipei 115, Taiwan
| | - Susan D Arco
- Institute of Chemistry, University of the Philippines , Diliman Quezon City, Philippines
| | - Alexey I Nesvizhskii
- Department of Computational Medicine and Bioinformatics and Department of Pathology, University of Michigan Medical School , 1301 Catherine, Ann Arbor, Michigan 48109, United States
| | - Ting-Yi Sung
- Institute of Information Science, Academia Sinica , 128 Academia Road, Section 2, Taipei 115, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica , No. 128, Academia Road Sec. 2, Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University , 101, Sec 2, Kuang-Fu Road, Hsinchu 30013, Taiwan.,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica , No. 1, Roosevelt Road, Sec. 4, Taipei 10617, Taiwan
| |
Collapse
|
37
|
LC–MS-based quantification of intact proteins: perspective for clinical and bioanalytical applications. Bioanalysis 2015; 7:1943-58. [DOI: 10.4155/bio.15.113] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Bioanalytical LC–MS for protein quantification is traditionally based on enzymatic digestion of the target protein followed by absolute quantification of a specific signature peptide relative to a stable-isotope labeled analog. The enzymatic digestion, nonetheless, limits rapid method development, sample throughput and turnaround time, and, moreover, makes that essential information regarding the biological function of the intact protein is lost. The recent advancements in high-resolution MS instrumentation and improved sample preparation techniques dedicated to protein clean-up raise the question to what extent LC–MS can be applied for quantitative bioanalysis of intact proteins. This review provides an overview of current and potential applications of LC–MS for intact protein quantification as well as the main limitations and challenges for broad application.
Collapse
|
38
|
Parker SJ, Rost H, Rosenberger G, Collins BC, Malmström L, Amodei D, Venkatraman V, Raedschelders K, Van Eyk JE, Aebersold R. Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry. Mol Cell Proteomics 2015. [PMID: 26199342 DOI: 10.1074/mcp.o114.042267] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Accurate knowledge of retention time (RT) in liquid chromatography-based mass spectrometry data facilitates peptide identification, quantification, and multiplexing in targeted and discovery-based workflows. Retention time prediction is particularly important for peptide analysis in emerging data-independent acquisition (DIA) experiments such as SWATH-MS. The indexed RT approach, iRT, uses synthetic spiked-in peptide standards (SiRT) to set RT to a unit-less scale, allowing for normalization of peptide RT between different samples and chromatographic set-ups. The obligatory use of SiRTs can be costly and complicates comparisons and data integration if standards are not included in every sample. Reliance on SiRTs also prevents the inclusion of archived mass spectrometry data for generation of the peptide assay libraries central to targeted DIA-MS data analysis. We have identified a set of peptide sequences that are conserved across most eukaryotic species, termed Common internal Retention Time standards (CiRT). In a series of tests to support the appropriateness of the CiRT-based method, we show: (1) the CiRT peptides normalized RT in human, yeast, and mouse cell lysate derived peptide assay libraries and enabled merging of archived libraries for expanded DIA-MS quantitative applications; (2) CiRTs predicted RT in SWATH-MS data within a 2-min margin of error for the majority of peptides; and (3) normalization of RT using the CiRT peptides enabled the accurate SWATH-MS-based quantification of 340 synthetic isotopically labeled peptides that were spiked into either human or yeast cell lysate. To automate and facilitate the use of these CiRT peptide lists or other custom user-defined internal RT reference peptides in DIA workflows, an algorithm was designed to automatically select a high-quality subset of datapoints for robust linear alignment of RT for use. Implementations of this algorithm are available for the OpenSWATH and Skyline platforms. Thus, CiRT peptides can be used alone or as a complement to SiRTs for RT normalization across peptide spectral libraries and in quantitative DIA-MS studies.
Collapse
Affiliation(s)
- Sarah J Parker
- ‡‡Advanced Clinical Biosystems Research Institute, The Heart Institute, and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Hannes Rost
- §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; ¶PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - George Rosenberger
- §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; ¶PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Ben C Collins
- §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | | | - Vidya Venkatraman
- ‡‡Advanced Clinical Biosystems Research Institute, The Heart Institute, and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Koen Raedschelders
- ‡‡Advanced Clinical Biosystems Research Institute, The Heart Institute, and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jennifer E Van Eyk
- From the ‡Department of Medicine, Johns Hopkins University, Baltimore Maryland; ‡‡Advanced Clinical Biosystems Research Institute, The Heart Institute, and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Ruedi Aebersold
- §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; §§Faculty of Science, University of Zurich, Zurich, Switzerland
| |
Collapse
|
39
|
Keller A, Bader SL, Shteynberg D, Hood L, Moritz RL. Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data-independent Acquisition Mass Spectrometry (MS) using SWATHProphet. Mol Cell Proteomics 2015; 14:1411-8. [PMID: 25713123 DOI: 10.1074/mcp.o114.044917] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Indexed: 11/06/2022] Open
Abstract
Proteomics by mass spectrometry technology is widely used for identifying and quantifying peptides and proteins. The breadth and sensitivity of peptide detection have been advanced by the advent of data-independent acquisition mass spectrometry. Analysis of such data, however, is challenging due to the complexity of fragment ion spectra that have contributions from multiple co-eluting precursor ions. We present SWATHProphet software that identifies and quantifies peptide fragment ion traces in data-independent acquisition data, provides accurate probabilities to ensure results are correct, and automatically detects and removes contributions to quantitation originating from interfering precursor ions. Integration in the widely used open source Trans-Proteomic Pipeline facilitates subsequent analyses such as combining results of multiple data sets together for improved discrimination using iProphet and inferring sample proteins using ProteinProphet. This novel development should greatly help make data-independent acquisition mass spectrometry accessible to large numbers of users.
Collapse
Affiliation(s)
- Andrew Keller
- From the Institute for Systems Biology, Seattle, Washington 98109
| | - Samuel L Bader
- From the Institute for Systems Biology, Seattle, Washington 98109
| | - David Shteynberg
- From the Institute for Systems Biology, Seattle, Washington 98109
| | - Leroy Hood
- From the Institute for Systems Biology, Seattle, Washington 98109
| | - Robert L Moritz
- From the Institute for Systems Biology, Seattle, Washington 98109
| |
Collapse
|
40
|
Building high-quality assay libraries for targeted analysis of SWATH MS data. Nat Protoc 2015; 10:426-41. [PMID: 25675208 DOI: 10.1038/nprot.2015.015] [Citation(s) in RCA: 220] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Targeted proteomics by selected/multiple reaction monitoring (S/MRM) or, on a larger scale, by SWATH (sequential window acquisition of all theoretical spectra) MS (mass spectrometry) typically relies on spectral reference libraries for peptide identification. Quality and coverage of these libraries are therefore of crucial importance for the performance of the methods. Here we present a detailed protocol that has been successfully used to build high-quality, extensive reference libraries supporting targeted proteomics by SWATH MS. We describe each step of the process, including data acquisition by discovery proteomics, assertion of peptide-spectrum matches (PSMs), generation of consensus spectra and compilation of MS coordinates that uniquely define each targeted peptide. Crucial steps such as false discovery rate (FDR) control, retention time normalization and handling of post-translationally modified peptides are detailed. Finally, we show how to use the library to extract SWATH data with the open-source software Skyline. The protocol takes 2-3 d to complete, depending on the extent of the library and the computational resources available.
Collapse
|
41
|
Bauer M, Ahrné E, Baron AP, Glatter T, Fava LL, Santamaria A, Nigg EA, Schmidt A. Evaluation of Data-Dependent and -Independent Mass Spectrometric Workflows for Sensitive Quantification of Proteins and Phosphorylation Sites. J Proteome Res 2014; 13:5973-88. [DOI: 10.1021/pr500860c] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Manuel Bauer
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Erik Ahrné
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Anna P. Baron
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Timo Glatter
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Luca L. Fava
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Anna Santamaria
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Erich A. Nigg
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Alexander Schmidt
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| |
Collapse
|
42
|
Abstract
New technologies in mass spectrometry are beginning to mature and show unique advantages for the identification and quantitation of proteins. In recent years, one of the significant goals of clinical proteomics has been to identify biomarkers that can be used for clinical diagnosis. As technology has progressed, the list of potential biomarkers has grown. However, the verification and validation of these potential biomarkers is increasingly challenging and require high-throughput quantitative assays, targeting specific candidates. Targeted proteomics bridges the gap between biomarker discovery and the development of clinically applicable biomarker assays.
Collapse
Affiliation(s)
- Robert Harlan
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | | |
Collapse
|
43
|
Rosenberger G, Koh CC, Guo T, Röst HL, Kouvonen P, Collins BC, Heusel M, Liu Y, Caron E, Vichalkovski A, Faini M, Schubert OT, Faridi P, Ebhardt HA, Matondo M, Lam H, Bader SL, Campbell DS, Deutsch EW, Moritz RL, Tate S, Aebersold R. A repository of assays to quantify 10,000 human proteins by SWATH-MS. Sci Data 2014; 1:140031. [PMID: 25977788 PMCID: PMC4322573 DOI: 10.1038/sdata.2014.31] [Citation(s) in RCA: 297] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/06/2014] [Indexed: 12/30/2022] Open
Abstract
Mass spectrometry is the method of choice for deep and reliable exploration of the (human) proteome. Targeted mass spectrometry reliably detects and quantifies pre-determined sets of proteins in a complex biological matrix and is used in studies that rely on the quantitatively accurate and reproducible measurement of proteins across multiple samples. It requires the one-time, a priori generation of a specific measurement assay for each targeted protein. SWATH-MS is a mass spectrometric method that combines data-independent acquisition (DIA) and targeted data analysis and vastly extends the throughput of proteins that can be targeted in a sample compared to selected reaction monitoring (SRM). Here we present a compendium of highly specific assays covering more than 10,000 human proteins and enabling their targeted analysis in SWATH-MS datasets acquired from research or clinical specimens. This resource supports the confident detection and quantification of 50.9% of all human proteins annotated by UniProtKB/Swiss-Prot and is therefore expected to find wide application in basic and clinical research. Data are available via ProteomeXchange (PXD000953-954) and SWATHAtlas (SAL00016-35).
Collapse
Affiliation(s)
- George Rosenberger
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; PhD Program in Systems Biology, University of Zurich and ETH Zurich , CH-8093 Zurich, Switzerland
| | - Ching Chiek Koh
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; Ruprecht Karls University of Heidelberg , DE-69117 Heidelberg, Germany
| | - Tiannan Guo
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Hannes L Röst
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; PhD Program in Systems Biology, University of Zurich and ETH Zurich , CH-8093 Zurich, Switzerland
| | - Petri Kouvonen
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Moritz Heusel
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; PhD Program in Molecular and Translational Biomedicine, Competence Centre for Systems Physiology and Metabolic Diseases (CC-SPMD), University of Zurich and ETH Zurich , CH-8093 Zurich, Switzerland
| | - Yansheng Liu
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Etienne Caron
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Anton Vichalkovski
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Marco Faini
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Olga T Schubert
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; PhD Program in Systems Biology, University of Zurich and ETH Zurich , CH-8093 Zurich, Switzerland
| | - Pouya Faridi
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; Department of Phytopharmaceuticals (Traditional Pharmacy), School of Pharmacy and Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, 71345-1583 Shiraz, Iran
| | - H Alexander Ebhardt
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Mariette Matondo
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Henry Lam
- Division of Biomedical Engineering and Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay , Hong Kong, China
| | - Samuel L Bader
- Institute for Systems Biology , Seattle, Washington 98109-5234, USA
| | - David S Campbell
- Institute for Systems Biology , Seattle, Washington 98109-5234, USA
| | - Eric W Deutsch
- Institute for Systems Biology , Seattle, Washington 98109-5234, USA
| | - Robert L Moritz
- Institute for Systems Biology , Seattle, Washington 98109-5234, USA
| | | | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; Faculty of Science, University of Zurich , CH-8057 Zurich, Switzerland
| |
Collapse
|
44
|
A targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins. Metab Eng 2014; 26:48-56. [PMID: 25205128 DOI: 10.1016/j.ymben.2014.08.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 08/06/2014] [Accepted: 08/28/2014] [Indexed: 11/20/2022]
Abstract
Transformation of engineered Escherichia coli into a robust microbial factory is contingent on precise control of metabolism. Yet, the throughput of omics technologies used to characterize cell components has lagged far behind our ability to engineer novel strains. To expand the utility of quantitative proteomics for metabolic engineering, we validated and optimized targeted proteomics methods for over 400 proteins from more than 20 major pathways in E. coli metabolism. Complementing these methods, we constructed a series of synthetic genes to produce concatenated peptides (QconCAT) for absolute quantification of the proteins and made them available through the Addgene plasmid repository (www.addgene.org). To facilitate high sample throughput, we developed a fast, analytical-flow chromatography method using a 5.5-min gradient (10 min total run time). Overall this toolkit provides an invaluable resource for metabolic engineering by increasing sample throughput, minimizing development time and providing peptide standards for absolute quantification of E. coli proteins.
Collapse
|
45
|
Qeli E, Omasits U, Goetze S, Stekhoven DJ, Frey JE, Basler K, Wollscheid B, Brunner E, Ahrens CH. Improved prediction of peptide detectability for targeted proteomics using a rank-based algorithm and organism-specific data. J Proteomics 2014; 108:269-83. [DOI: 10.1016/j.jprot.2014.05.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 05/14/2014] [Accepted: 05/17/2014] [Indexed: 02/07/2023]
|
46
|
Heikkinen AT, Friedlein A, Matondo M, Hatley OJD, Petsalo A, Juvonen R, Galetin A, Rostami-Hodjegan A, Aebersold R, Lamerz J, Dunkley T, Cutler P, Parrott N. Quantitative ADME Proteomics – CYP and UGT Enzymes in the Beagle Dog Liver and Intestine. Pharm Res 2014; 32:74-90. [DOI: 10.1007/s11095-014-1446-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 07/02/2014] [Indexed: 12/16/2022]
|
47
|
Broudy D, Killeen T, Choi M, Shulman N, Mani DR, Abbatiello SE, Mani D, Ahmad R, Sahu AK, Schilling B, Tamura K, Boss Y, Sharma V, Gibson BW, Carr SA, Vitek O, MacCoss MJ, MacLean B. A framework for installable external tools in Skyline. Bioinformatics 2014; 30:2521-3. [PMID: 24813211 DOI: 10.1093/bioinformatics/btu148] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
UNLABELLED Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. The Skyline document model contains extensive mass spectrometry data from targeted proteomics experiments performed using selected reaction monitoring, parallel reaction monitoring and data-independent and data-dependent acquisition methods. Researchers have developed software tools that perform statistical analysis of the experimental data contained within Skyline documents. The new external tools framework allows researchers to integrate their tools into Skyline without modifying the Skyline codebase. Installed tools provide point-and-click access to downstream statistical analysis of data processed in Skyline. The framework also specifies a uniform interface to format tools for installation into Skyline. Tool developers can now easily share their tools with proteomics researchers using Skyline. AVAILABILITY AND IMPLEMENTATION Skyline is available as a single-click self-updating web installation at http://skyline.maccosslab.org. This Web site also provides access to installable external tools and documentation. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Daniel Broudy
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Trevor Killeen
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Meena Choi
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Nicholas Shulman
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Deepak R Mani
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Susan E Abbatiello
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Deepak Mani
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Rushdy Ahmad
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Alexandria K Sahu
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Birgit Schilling
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Kaipo Tamura
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Yuval Boss
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Vagisha Sharma
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Bradford W Gibson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Steven A Carr
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Olga Vitek
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Brendan MacLean
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, Department of Statistics, Purdue University, West Lafayette, IN 47907, Broad Institute of MIT and Harvard, Cambridge, MA 02142 and Buck Institute for Research on Aging, Novato, CA 94945, USA
| |
Collapse
|
48
|
Amory JK, Arnold S, Lardone MC, Piottante A, Ebensperger M, Isoherranen N, Muller CH, Walsh T, Castro A. Levels of the retinoic acid synthesizing enzyme aldehyde dehydrogenase-1A2 are lower in testicular tissue from men with infertility. Fertil Steril 2014; 101:960-6. [PMID: 24524833 PMCID: PMC3972330 DOI: 10.1016/j.fertnstert.2013.12.053] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 12/30/2013] [Accepted: 12/30/2013] [Indexed: 12/23/2022]
Abstract
OBJECTIVE To determine whether decreased testicular levels of enzymes necessary for retinoic acid biosynthesis were associated with male infertility, as retinoic acid is known to be necessary for spermatogenesis. DESIGN Observational analysis of testicular tissue samples, sperm indices, and serum hormone concentrations. SETTING Two infertility centers in Chile. PATIENT(S) 32 infertile men and 11 control men. INTERVENTION(S) Measurement of the three enzymes necessary for retinoic acid biosynthesis, aldehyde dehydrogenase (ALDH) 1A1, 1A2, and 1A3, in testicular tissue by a novel liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) peptide assay. MAIN OUTCOME MEASURE(S) ALDH isozyme levels compared by type of infertility and correlated with testicular germ cell numbers, sperm parameters, and serum and intratesticular hormone concentrations. RESULT(S) Men with infertility had statistically significantly reduced levels of ALDH1A2 but not ALDH1A1 or ALDH1A3 in their testicular tissue compared with men with normal spermatogenesis. The ALDH1A2 protein levels were strongly correlated with the number of germ cells found via testicular biopsy. CONCLUSION(S) These findings suggest that ALDH1A2 is the enzyme involved in retinoic acid biosynthesis in human germ cells. Further study of the relationship between intratesticular ALDH1A2 and male infertility is warranted to determine whether men with infertility have a reduced ability to synthesize retinoic acid within their germ cells that could impair spermatogenesis.
Collapse
Affiliation(s)
- John K Amory
- Department of Medicine, University of Washington, Seattle, Washington.
| | - Samuel Arnold
- Department of Pharmaceutics, University of Washington, Seattle, Washington
| | - María C Lardone
- Institute of Maternal and Child Research, School of Medicine, University of Chile, Santiago, Chile
| | | | | | - Nina Isoherranen
- Department of Pharmaceutics, University of Washington, Seattle, Washington
| | - Charles H Muller
- Department of Urology, University of Washington, Seattle, Washington
| | - Thomas Walsh
- Department of Urology, University of Washington, Seattle, Washington
| | - Andrea Castro
- Institute of Maternal and Child Research, School of Medicine, University of Chile, Santiago, Chile
| |
Collapse
|
49
|
Chen C, Liu X, Zheng W, Zhang L, Yao J, Yang P. Screening of missing proteins in the human liver proteome by improved MRM-approach-based targeted proteomics. J Proteome Res 2014; 13:1969-78. [PMID: 24597967 DOI: 10.1021/pr4010986] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
To completely annotate the human genome, the task of identifying and characterizing proteins that currently lack mass spectrometry (MS) evidence is inevitable and urgent. In this study, as the first effort to screen missing proteins in large scale, we developed an approach based on SDS-PAGE followed by liquid chromatography-multiple reaction monitoring (LC-MRM), for screening of those missing proteins with only a single peptide hit in the previous liver proteome data set. Proteins extracted from normal human liver were separated in SDS-PAGE and digested in split gel slice, and the resulting digests were then subjected to LC-schedule MRM analysis. The MRM assays were developed through synthesized crude peptides for target peptides. In total, the expressions of 57 target proteins were confirmed from 185 MRM assays in normal human liver tissues. Among the proved 57 one-hit wonders, 50 proteins are of the minimally redundant set in the PeptideAtlas database, 7 proteins even have none MS-based information previously in various biological processes. We conclude that our SDS-PAGE-MRM workflow can be a powerful approach to screen missing or poorly characterized proteins in different samples and to provide their quantity if detected. The MRM raw data have been uploaded to ISB/SRM Atlas/PASSEL (PXD000648).
Collapse
Affiliation(s)
- Chen Chen
- Department of Chemistry, Fudan University , Shanghai 200032, P. R. China
| | | | | | | | | | | |
Collapse
|
50
|
OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nat Biotechnol 2014; 32:219-23. [DOI: 10.1038/nbt.2841] [Citation(s) in RCA: 547] [Impact Index Per Article: 54.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|