Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

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Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

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Absolute Quantification of Proteins by LCMSE

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Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

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Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues

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MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments

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OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

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DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

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Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry

Collins, B. C., Hunter, C. L., Liu, Y., Schilling, B., Rosenberger, G., Bader, S. L., Chan, D. W., Gibson, B. W., Gingras, A.-C., Held, J. M., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00249-5 · Cited by 576

Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometry-based Assay Development Using a Fit-for-Purpose Approach

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Targeted Proteomic Quantification on Quadrupole-Orbitrap Mass Spectrometer

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Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry

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A repository of assays to quantify 10,000 human proteins by SWATH-MS

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A multicenter study benchmarks software tools for label-free proteome quantification

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Quantitative variability of 342 plasma proteins in a human twin population

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Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition

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Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system

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Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome

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Precursor Acquisition Independent From Ion Count: How to Dive Deeper into the Proteomics Ocean

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Reproducible Quantification of Cancer-Associated Proteins in Body Fluids Using Targeted Proteomics

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Mass spectrometry based biomarker discovery, verification, and validation — Quality assurance and control of protein biomarker assays

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Building ProteomeTools based on a complete synthetic human proteome

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Panorama: A Targeted Proteomics Knowledge Base

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Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma

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Multiplexed peptide analysis using data-independent acquisition and Skyline

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Using data‐independent, high‐resolution mass spectrometry in protein biomarker research: Perspectives and clinical applications

Sajic, T., Liu, Y., & Aebersold, R. H. (2014) · PROTEOMICS - CLINICAL APPLICATIONS · doi:10.1002/prca.201400117 · Cited by 214

Technical considerations for large-scale parallel reaction monitoring analysis

Gallien, S., Bourmaud, A., Kim, S.-Y., & Domon, B. (2013) · Journal of Proteomics · doi:10.1016/j.jprot.2013.10.029 · Cited by 209

Quantitative measurements of N‐linked glycoproteins in human plasma by SWATH‐MS

Liu, Y., Hüttenhain, R., Surinova, S., Gillet, L. C., Mouritsen, J., Brunner, R., Navarro, P., & Aebersold, R. (2013) · PROTEOMICS · doi:10.1002/pmic.201200417 · Cited by 204

The Use of Variable Q1 Isolation Windows Improves Selectivity in LC–SWATH–MS Acquisition

Zhang, Y., Pena, A. B., Bruderer, T., Luban, J., Strambio‐De‐Castillia, C., Lisacek, F., Gérard Hopfgartner, D., & Varesio, E. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00543 · Cited by 201

Processing strategies and software solutions for data‐independent acquisition in mass spectrometry

Pena, A. B., Varesio, E., Luban, J., Strambio‐De‐Castillia, C., Gérard Hopfgartner, D., Müller, M., & Lisacek, F. (2014) · PROTEOMICS · doi:10.1002/pmic.201400323 · Cited by 196

Glycoproteomic Analysis of Prostate Cancer Tissues by SWATH Mass Spectrometry Discovers N-acylethanolamine Acid Amidase and Protein Tyrosine Kinase 7 as Signatures for Tumor Aggressiveness

Liu, Y., Chen, J., Sethi, A., Li, Q. K., Chen, L., Collins, B. C., Gillet, L. C. J., Wollscheid, B., Zhang, H., & Aebersold, R. H. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.038273 · Cited by 187

Reproducible and Consistent Quantification of the Saccharomyces cerevisiae Proteome by SWATH-mass spectrometry *

Selevsek, N., Chang, C.-Y., Gillet, L. C. J., Navarro, P., Bernhardt, O. M., Reiter, L., Cheng, L., Vitek, O., & Aebersold, R. H. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.035550 · Cited by 181

Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data

Ting, Y. S., Egertson, J. D., Payne, S. H., Kim, S., MacLean, B., Käll, L., Aebersold, R., Smith, R. D., Noble, W. S., & MacCoss, M. J. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o114.047035 · Cited by 175

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics

Röst, H. L., Liu, Y., D’Agostino, G. A., Zanella, M., Navarro, P., Rosenberger, G., Collins, B. C., Gillet, L. C. J., Testa, G., Malmström, L., et al. (2016) · Nature Methods · doi:10.1038/nmeth.3954 · Cited by 166

Advances in multiplexed MRM-based protein biomarker quantitation toward clinical utility

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mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry

Teo, G., Kim, S., Tsou, C., Collins, B. C., Gingras, A., Nesvizhskii, A. I., & Choi, H. (2015) · Journal of Proteomics · doi:10.1016/j.jprot.2015.09.013 · Cited by 139

Large‐scale multiplex absolute protein quantification of drug‐metabolizing enzymes and transporters in human intestine, liver, and kidney microsomes by SWATH‐MS: Comparison with MRM/SRM and HR‐MRM/PRM

Nakamura, K., Hirayama‐Kurogi, M., Ito, S., Kuno, T., Yoneyama, T., Obuchi, W., Terasaki, T., & Ohtsuki, S. (2016) · PROTEOMICS · doi:10.1002/pmic.201500433 · Cited by 138

Advancing Urinary Protein Biomarker Discovery by Data-Independent Acquisition on a Quadrupole-Orbitrap Mass Spectrometer

Muntel, J., Xuan, Y., Berger, S. T., Reiter, L., Bachur, R. G., Kentsis, A., & Steen, H. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00826 · Cited by 137

MSPLIT-DIA: sensitive peptide identification for data-independent acquisition

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Multiplexed, Scheduled, High-Resolution Parallel Reaction Monitoring on a Full Scan QqTOF Instrument with Integrated Data-Dependent and Targeted Mass Spectrometric Workflows

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Design, Implementation and Multisite Evaluation of a System Suitability Protocol for the Quantitative Assessment of Instrument Performance in Liquid Chromatography-Multiple Reaction Monitoring-MS (LC-MRM-MS)

Abbatiello, S. E., Mani, D. R., Schilling, B., MacLean, B., Zimmerman, L. J., Feng, X., Cusack, M. P., Sedransk, N., Hall, S. C., Addona, T. A., et al. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m112.027078 · Cited by 113

Method of the Year 2012

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Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH) Analysis for Characterization and Quantification of Histone Post-translational Modifications

Sidoli, S., Lin, S., Xiong, L., Bhanu, N. V., Karch, K. R., Johansen, E., Hunter, C. L., Mollah, S., & Garcia, B. A. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o114.046102 · Cited by 104

Group-DIA: analyzing multiple data-independent acquisition mass spectrometry data files

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XDIA: improving on the label-free data-independent analysis

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Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry

Parker, S. J., Röst, H. L., Rosenberger, G., Collins, B. C., Malmström, L., Amodei, D., Venkatraman, V., Raedschelders, K., Eyk, J. E. V., & Aebersold, R. H. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o114.042267 · Cited by 94

Discovery of potential protein biomarkers of lung adenocarcinoma in bronchoalveolar lavage fluid by SWATH MS data-independent acquisition and targeted data extraction

Ortea, I., Rodríguez‐Ariza, A., Chicano‐Gálvez, E., Vacas, M. S. A., & Gámez, B. J. (2016) · Journal of Proteomics · doi:10.1016/j.jprot.2016.02.010 · Cited by 81

Precise label-free quantitative proteomes in high-throughput by microLC and data-independent SWATH acquisition

Vowinckel, J., Zelezniak, A., Kibler, A., Bruderer, R., Muelleder, M., Reiter, L., & Ralser, M. (2016) · doi:10.1101/073478 · Cited by 81

Generation of High-Quality SWATH® Acquisition Data for Label-free Quantitative Proteomics Studies Using TripleTOF® Mass Spectrometers

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Quantification of lysine acetylation and succinylation stoichiometry in proteins using mass spectrometric data-independent acquisitions (SWATH)

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Cost-effective generation of precise label-free quantitative proteomes in high-throughput by microLC and data-independent acquisition

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Quantitative Proteomics by SWATH-MS Reveals Altered Expression of Nucleic Acid Binding and Regulatory Proteins in HIV-1-Infected Macrophages

Haverland, N. A., Fox, H. S., & Ciborowski, P. S. (2014) · Journal of Proteome Research · doi:10.1021/pr4012602 · Cited by 74

Quantification of SAHA-Dependent Changes in Histone Modifications Using Data-Independent Acquisition Mass Spectrometry

Krautkramer, K. A., Reiter, L., Denu, J. M., & Dowell, J. A. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00245 · Cited by 73

Untargeted, spectral library‐free analysis of data‐independent acquisition proteomics data generated using Orbitrap mass spectrometers

Tsou, C., Tsai, C., Teo, G. C., Chen, Y., & Nesvizhskii, A. I. (2016) · PROTEOMICS · doi:10.1002/pmic.201500526 · Cited by 73

Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays

Whiteaker, J. R., Halusa, G. N., Hoofnagle, A. N., Sharma, V., MacLean, B., Yan, P., Wrobel, J. A., Kennedy, J. J., Mani, D. R., Zimmerman, L. J., et al. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-3524-6_13 · Cited by 73

Applications and Developments in Targeted Proteomics: From SRM to DIA/SWATH

Aebersold, R. H., Bensimon, A., Collins, B. C., Ludwig, C., & Sabidó, E. (2016) · PROTEOMICS · doi:10.1002/pmic.201600203 · Cited by 72

Evaluation of proteomic biomarkers associated with circulating microparticles as an effective means to stratify the risk of spontaneous preterm birth

Cantonwine, D. E., Zhang, Z., Rosenblatt, K. P., Goudy, K., Doss, R. C., Ezrin, A. M., Page, G., Brohman, B., & McElrath, T. F. (2016) · American Journal of Obstetrics and Gynecology · doi:10.1016/j.ajog.2016.02.005 · Cited by 71

An Automated Pipeline to Monitor System Performance in Liquid Chromatography–Tandem Mass Spectrometry Proteomic Experiments

Bereman, M. S., Beri, J., Sharma, V., Nathe, C., Eckels, J., MacLean, B., & MacCoss, M. J. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00744 · Cited by 69

Detection and quantification of proteins in clinical samples using high resolution mass spectrometry

Gallien, S., & Domon, B. (2015) · Methods · doi:10.1016/j.ymeth.2015.03.015 · Cited by 65

Building the Connectivity Map of epigenetics: Chromatin profiling by quantitative targeted mass spectrometry

Creech, A. L., Taylor, J. E., Maier, V., Wu, X., Feeney, C. M., Udeshi, N. D., Peach, S. E., Boehm, J. S., Lee, J. T., Carr, S. A., et al. (2014) · Methods · doi:10.1016/j.ymeth.2014.10.033 · Cited by 62

Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometryPreprint

Collins, B. C., Hunter, C. L., Liu, Y., et al. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/074567 · Cited by 59

Understanding the dimorphic lifestyles of human gastric pathogen Helicobacter pylori using the SWATH-based proteomics approach

Loke, M. F., Ng, C. G., Vilashni, Y., Lim, J. W. E., & Ho, B. (2016) · Scientific Reports · doi:10.1038/srep26784 · Cited by 57

SWATH analysis of the synaptic proteome in Alzheimer's disease

Chang, R. Y. K., Etheridge, N., Nouwens, A. S., & Dodd, P. R. (2015) · Neurochemistry International · doi:10.1016/j.neuint.2015.04.004 · Cited by 56

Assessment of SRM, MRM3, and DIA for the targeted analysis of phosphorylation dynamics in non‐small cell lung cancer

Schmidlin, T., Garrigues, L., Lane, C. S., Mulder, T., van Doorn, S., Post, H., de Graaf, E. L., Lemeer, S., Heck, A. J. R., & Altelaar, M. A. F. (2016) · PROTEOMICS · doi:10.1002/pmic.201500453 · Cited by 53

Minimal sample requirement for highly multiplexed protein quantification in cell lines and tissues by PCT‐SWATH mass spectrometry

Shao, S., Guo, T., Koh, C. C., Gillessen, S., Joerger, M., Jochum, W., & Aebersold, R. H. (2015) · PROTEOMICS · doi:10.1002/pmic.201500161 · Cited by 48

Biomarker Discovery and Verification of Esophageal Squamous Cell Carcinoma Using Integration of SWATH/MRM

Hou, G., Lou, X., Sun, Y., Xu, S., Zi, J., Wang, Q., Zhou, B., Han, B. H., Wu, L., Zhao, X., et al. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00438 · Cited by 48

Clinical translation of MS-based, quantitative plasma proteomics: status, challenges, requirements, and potential

Percy, A. J., Byrns, S., Pennington, S. R., Holmes, D. T., Anderson, N. L., Agreste, T. M., & Duffy, M. A. (2016) · Expert Review of Proteomics · doi:10.1080/14789450.2016.1205950 · Cited by 47

Targeted proteomics coming of age – SRM, PRM and DIA performance evaluated from a core facility perspective

Kockmann, T., Trachsel, C., Panse, C., Wåhlander, Å., Selevsek, N., Grossmann, J., Wolski, W., & Schlapbach, R. (2016) · PROTEOMICS · doi:10.1002/pmic.201500502 · Cited by 45

Opening a SWATH Window on Posttranslational Modifications: Automated Pursuit of Modified Peptides

Keller, A., Bader, S. L., Kusebauch, U., Shteynberg, D. D., Hood, L., & Moritz, R. L. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m115.054478 · Cited by 39

Tools for monitoring system suitability in LC MS/MS centric proteomic experiments

Bereman, M. S. (2014) · PROTEOMICS · doi:10.1002/pmic.201400373 · Cited by 36

A framework for installable external tools in Skyline

Broudy, D., Killeen, T., Choi, M., Shulman, N., Mani, D. R., Abbatiello, S. E., Mani, D. R., Ahmad, R., Sahu, A. K., Schilling, B., et al. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu148 · Cited by 34

Identifying Urinary and Serum Exosome Biomarkers for Radiation Exposure Using a Data Dependent Acquisition and SWATH-MS Combined Workflow

Kulkarni, S. S., Koller, A. A., Mani, K. M., Wen, R., Alfieri, A. A., Saha, S., Wang, J., Patel, P. R., Bandeira, N., Guha, C., et al. (2016) · International Journal of Radiation Oncology*Biology*Physics · doi:10.1016/j.ijrobp.2016.06.008 · Cited by 32

Quantitative proteogenomics of human pathogens using DIA-MS

Malmström, L., Bakochi, A., Svensson, G., Kilsgård, O., Lantz, H., Petersson, A. C., Hauri, S., Karlsson, C. A. Q., & Malmström, J. A. (2015) · Journal of Proteomics · doi:10.1016/j.jprot.2015.09.012 · Cited by 29

Variation and quantification among a target set of phosphopeptides in human plasma by multiple reaction monitoring and SWATH‐MS2 data‐independent acquisition

Zawadzka, A. M., Schilling, B., Held, J. M., Sahu, A. K., Cusack, M. P., Drake, P. M., Fisher, S. J., & Gibson, B. W. (2014) · Electrophoresis · doi:10.1002/elps.201400167 · Cited by 24

Mass Spectral Enhanced Detection of Ubls Using SWATH Acquisition: MEDUSA—Simultaneous Quantification of SUMO and Ubiquitin-Derived Isopeptides

Griffiths, J. R., Chicooree, N., Connolly, Y., Neffling, M.-R., Lane, C. S., Knapman, T., & Smith, D. L. (2014) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-014-0835-x · Cited by 23

Rapid label‐free profiling of oral cancer biomarker proteins using nano‐UPLC‐Q‐TOF ion mobility mass spectrometry

Nassar, A. F., Williams, B. J., Yaworksy, D. C., Patel, V., & Rusling, J. F. (2015) · PROTEOMICS - CLINICAL APPLICATIONS · doi:10.1002/prca.201500025 · Cited by 23

Applying SWATH Mass Spectrometry to Investigate Human Cervicovaginal Fluid During the Menstrual Cycle1

Vaswani, K., Ashman, K., Reed, S., Salomón, C., Sarker, S., Arraztoa, J. A., Pérez‐Sepúlveda, A., Illanes, S. E., Kvaskoff, D., Mitchell, M. D., et al. (2015) · Biology of Reproduction · doi:10.1095/biolreprod.115.128231 · Cited by 17

A reference library of peripheral blood mononuclear cells for SWATH‐MS analysis

Silva, C. S., Santa, C., Anjo, S. I., & Manadas, B. J. (2016) · PROTEOMICS - CLINICAL APPLICATIONS · doi:10.1002/prca.201600070 · Cited by 16

Multiple Biomarker Panels for Early Detection of Breast Cancer in Peripheral Blood

Zhang, F., Deng, Y., & Drabier, R. (2013) · BioMed Research International · doi:10.1155/2013/781618 · Cited by 12

Quantifying the human proteome

Paulovich, A. G., & Whiteaker, J. R. (2016) · Nature Biotechnology · doi:10.1038/nbt.3695 · Cited by 11

p-SRM, SWATH and HRM – Targeted Proteomics Approaches on TripleTOF 5600+ Mass Spectrometer and Th eir Applications in Oncology Research

Faktor, J., Michalová, E., & Bouchal, P. (2014) · Klinicka onkologie · doi:10.14735/amko20141s110 · Cited by 4

Peptides aplenty

Doerr, A. J. (2013) · Nature Methods · doi:10.1038/nmeth.2548 · Cited by 2

The Mitochondrial Acylome Emerges: Proteomics, Regulation by Sirtuins, and Metabolic and Disease Implications

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Recent advances in mass spectrometry based clinical proteomics: applications to cancer research

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Understanding interactions between biomaterials and biological systems using proteomics

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Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry

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Application of targeted mass spectrometry in bottom-up proteomics for systems biology research

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Advances in targeted proteomics and applications to biomedical research

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Exploring the Potential of Data-Independent Acquisition Proteomics Using Untargeted All-Ion Quantitation: Application to Tumor Subtype Diagnosis

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A review on mass spectrometry-based quantitative proteomics: targeted and data independent acquisition

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Using data‐independent, high‐resolution mass spectrometry in protein biomarker research: Perspectives and clinical applications

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Evaluation of SRM-, PRM- and DIA-based Targeted Quantification

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