Biomedical applications of ion mobility-enhanced data-independent acquisition-based label-free quantitative proteomics

References

• Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 2003;422:198-207
   PubMed Web of Science ®Google Scholar
• Mallick P, Kuster B. Proteomics: a pragmatic perspective. Nat Biotechnol 2010;28:695-709
   PubMed Web of Science ®Google Scholar
• Wilhelm M, Schlegl J, Hahne H, et al. Mass-spectrometry-based draft of the human proteome. Nature 2014;509:582-7
   PubMed Web of Science ®Google Scholar
• Kim M-S, Pinto SM, Getnet D, et al. A draft map of the human proteome. Nature 2014;509:575-81
   PubMed Web of Science ®Google Scholar
• Liu H, Sadygov RG, Yates JR. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 2004;76:4193-201
   PubMed Web of Science ®Google Scholar
• Geromanos SJ, Vissers JPC, Silva JC, et al. The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS. Proteomics 2009;9:1683-95
   PubMed Web of Science ®Google Scholar
• Michalski A, Cox J, Mann M. More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J Proteome Res 2011;10:1785-93
   PubMed Web of Science ®Google Scholar
• Venable JD, Dong M, Wohlschlegel J, et al. Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat Methods 2004;1:39-45
   PubMed Web of Science ®Google Scholar
• Geiger T, Cox J, Mann M. Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation. Mol Cell Proteomics 2010;9:2252-61
   PubMed Web of Science ®Google Scholar
• Panchaud A, Jung S, Shaffer Sa, et al. Faster, quantitative, and accurate precursor acquisition independent from ion count. Anal Chem 2011;83:2250-7
   PubMed Web of Science ®Google Scholar
• Gillet LC, Navarro P, Tate S, et al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics 2012;11:O111.016717
   PubMed Web of Science ®Google Scholar
• Silva JC, Denny R, Dorschel C, et al. Quantitative proteomic analysis by accurate mass retention time pairs. Anal Chem 2005;77:2187-200
   PubMed Web of Science ®Google Scholar
• Panchaud A, Scherl A, Shaffer SA, et al. Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. Anal Chem 2009;81:6481-8
   PubMed Web of Science ®Google Scholar
• Purvine S, Eppel J-T, Yi EC, Goodlett DR. Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer. Proteomics 2003;3:847-50
   PubMed Web of Science ®Google Scholar
• Carvalho PC, Han X, Xu T, et al. XDIA: improving on the label-free data-independent analysis. Bioinformatics 2010;26:847-8
   PubMed Web of Science ®Google Scholar
• Egertson JD, Kuehn A, Merrihew GE, et al. Multiplexed MS/MS for improved data-independent acquisition. Nat Methods 2013;10:744-6
   PubMed Web of Science ®Google Scholar
• Weisbrod CR, Eng JK, Hoopmann MR, et al. Accurate peptide fragment mass analysis: multiplexed peptide identification and quantification. J Proteome Res 2012;11:1621-32
   Google Scholar
• Ramos AA, Yang H, Rosen LE, Yao X. Tandem parallel fragmentation of peptides for mass spectrometry. Anal Chem 2006;78:6391-7
   Google Scholar
• Law KP, Lim YP. Recent advances in mass spectrometry: data independent analysis and hyper reaction monitoring. Expert Rev Proteomics 2013;10:551-66
   PubMed Web of Science ®Google Scholar
• Chapman JD, Goodlett DR, Masselon CD. Multiplexed and data-independent tandem mass spectrometry for global proteome profiling. Mass Spectrom Rev 2013. [Epub ahead of print]
   PubMed Web of Science ®Google Scholar
• Silva JC, Gorenstein M V, Li G-Z, et al. Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Mol Cell Proteomics 2006;5:144-56
   PubMed Web of Science ®Google Scholar
• Neilson KA, Ali NA, Muralidharan S, et al. Less label, more free: approaches in label-free quantitative mass spectrometry. Proteomics 2011;11:535-53
   PubMed Web of Science ®Google Scholar
• Carroll KM, Simpson DM, Eyers CE, et al. Absolute quantification of the glycolytic pathway in yeast: deployment of a complete QconCAT approach. Mol Cell Proteomics 2011;10:M111.007633
   PubMed Web of Science ®Google Scholar
• Schwanhäusser B, Busse D, Li N, et al. Global quantification of mammalian gene expression control. Nature 2011;473:337-42
   PubMed Web of Science ®Google Scholar
• Colaert N, Gevaert K, Martens L. RIBAR and xRIBAR: methods for reproducible relative MS/MS-based label-free protein quantification. J Proteome Res 2011;10:3183-9
   Google Scholar
• Arike L, Valgepea K, Peil L, et al. Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli. J Proteomics 2012;75:5437-48
   PubMed Web of Science ®Google Scholar
• Filiou MD, Martins-de-Souza D, Guest PC, et al. To label or not to label: applications of quantitative proteomics in neuroscience research. Proteomics 2012;12:736-47
   Google Scholar
• Nahnsen S, Bielow C, Reinert K, Kohlbacher O. Tools for label-free peptide quantification. Mol Cell Proteomics 2013;12:549-56
   PubMed Web of Science ®Google Scholar
• Tate S, Larsen B, Bonner R, Gingras A-C. Label-free quantitative proteomics trends for protein-protein interactions. J Proteomics 2013;81:91-101
   Google Scholar
• Evans C, Noirel J, Ow SY, et al. An insight into iTRAQ: where do we stand now? Anal Bioanal Chem 2012;404:1011-27
   PubMed Web of Science ®Google Scholar
• Hakimi A, Auluck J, Jones GD, et al. Assessment of reproducibility in depletion and enrichment workflows for plasma proteomics using label-free quantitative data-independent LC-MS. Proteomics 2014;14:4-13
   Google Scholar
• Turtoi A, Mazzucchelli GD, De Pauw E. Isotope coded protein label quantification of serum proteins–comparison with the label-free LC-MS and validation using the MRM approach. Talanta 2010;80:1487-95
   PubMed Web of Science ®Google Scholar
• Levin Y, Jaros JAJ, Schwarz E, Bahn S. Multidimensional protein fractionation of blood proteins coupled to data-independent nanoLC-MS/MS analysis. J Proteomics 2010;73:689-95
   PubMed Web of Science ®Google Scholar
• Da Silva BF, Souza GHMF, lo Turco EG, et al. Differential seminal plasma proteome according to semen retrieval in men with spinal cord injury. Fertil Steril 2013;100:959-69
   PubMed Web of Science ®Google Scholar
• Foster MW, Thompson JW, Que LG, et al. Proteomic analysis of human bronchoalveolar lavage fluid after subsgemental exposure. J Proteome Res 2013;12:2194-205
   Google Scholar
• Martens GA, Jiang L, Verhaeghen K, et al. Protein markers for insulin-producing beta cells with higher glucose sensitivity. PLoS ONE 2010;5:e14214
   Google Scholar
• Oswald ES, Brown LM, Bulinski JC, Hung CT. Label-free protein profiling of adipose-derived human stem cells under hyperosmotic treatment. J Proteome Res 2011;10:3050-9
   Google Scholar
• Lee J-E, Park J-H, Moon P-G, Baek M-C. Identification of differentially expressed proteins by treatment with PUGNAc in 3T3-L1 adipocytes through analysis of ATP-binding proteome. Proteomics 2013;13:2998-3012
   Google Scholar
• Stelzhammer V, Amess B, Martins-de-Souza D, et al. Analysis of the rat hypothalamus proteome by data-independent label-free LC-MS/MS. Proteomics 2012;12:3386-92
   Google Scholar
• Martins-de-Souza D, Guest PC, Harris LW, et al. Identification of proteomic signatures associated with depression and psychotic depression in post-mortem brains from major depression patients. Transl Psychiatry 2012;2:e87
   PubMed Web of Science ®Google Scholar
• Krishnamurthy D, Levin Y, Harris LW, et al. Analysis of the human pituitary proteome by data independent label-free liquid chromatography tandem mass spectrometry. Proteomics 2011;11:495-500
   Google Scholar
• Rivers J, Hughes C, McKenna T, et al. Asymmetric proteome equalization of the skeletal muscle proteome using a combinatorial hexapeptide library. PLoS ONE 2011;6:e28902
   Google Scholar
• Werner HB, Krämer-Albers E-M, Strenzke N, et al. A critical role for the cholesterol-associated proteolipids PLP and M6B in myelination of the central nervous system. Glia 2013;61:567-86
   PubMed Web of Science ®Google Scholar
• Günther C, Martini E, Wittkopf N, et al. Caspase-8 regulates TNF-α-induced epithelial necroptosis and terminal ileitis. Nature 2011;477:335-9
   PubMed Web of Science ®Google Scholar
• Patzig J, Jahn O, Tenzer S, et al. Quantitative and integrative proteome analysis of peripheral nerve myelin identifies novel myelin proteins and candidate neuropathy loci. J Neurosci 2011;31:16369-86
   PubMed Web of Science ®Google Scholar
• Jahn O, Tenzer S, Werner HB. Myelin proteomics: molecular anatomy of an insulating sheath. Mol Neurobiol 2009;40:55-72
   PubMed Web of Science ®Google Scholar
• De Monasterio-Schrader P, Jahn O, Tenzer S, et al. Systematic approaches to central nervous system myelin. Cell Mol Life Sci 2012;69:2879-94
   PubMed Web of Science ®Google Scholar
• Reyda S, Büscher N, Tenzer S, Plachter B. Proteomic analyses of human cytomegalovirus strain AD169 derivatives reveal highly conserved patterns of viral and cellular proteins in infected fibroblasts. Viruses 2014;6:172-88
   Google Scholar
• Rodríguez-Suárez E, Gonzalez E, Hughes C, et al. Quantitative proteomic analysis of hepatocyte-secreted extracellular vesicles reveals candidate markers for liver toxicity. J Proteomics 2014;103:227-40
   Web of Science ®Google Scholar
• Krämer-Albers E-M, Bretz N, Tenzer S, et al. Oligodendrocytes secrete exosomes containing major myelin and stress-protective proteins: trophic support for axons? Proteomics Clin Appl 2007;1:1446-61
   PubMed Web of Science ®Google Scholar
• Brioschi M, Lento S, Tremoli E, Banfi C. Proteomic analysis of endothelial cell secretome: a means of studying the pleiotropic effects of Hmg-CoA reductase inhibitors. J Proteomics 2013;78:346-61
   Google Scholar
• Cortezzi SS, Garcia JS, Ferreira CR, et al. Secretome of the preimplantation human embryo by bottom-up label-free proteomics. Anal Bioanal Chem 2011;401:1331-9
   PubMed Web of Science ®Google Scholar
• Muntel J, Fromion V, Goelzer A, et al. Comprehensive absolute quantification of the cytosolic proteome of Bacillus subtilis by data independent, parallel fragmentation in liquid chromatography/mass spectrometry (LC/MS(E)). Mol Cell Proteomics 2014;13:1008-19
   PubMed Web of Science ®Google Scholar
• Terilli RR, Moura H, Woolfitt AR, et al. A historical and proteomic analysis of botulinum neurotoxin type/G. BMC Microbiol 2011;11:232
   Google Scholar
• Moura H, Terilli RR, Woolfitt AR, et al. Proteomic analysis and label-free quantification of the large Clostridium difficile toxins. Int J Proteomics 2013;2013:293782
   Google Scholar
• Levin Y, Hradetzky E, Bahn S. Quantification of proteins using data-independent analysis (MSE) in simple andcomplex samples: a systematic evaluation. Proteomics 2011;11:3273-87
   Google Scholar
• Silva JC, Denny R, Dorschel C, et al. Simultaneous qualitative and quantitative analysis of the Escherichia coli proteome: a sweet tale. Mol Cell Proteomics 2006;5:589-607
   PubMed Web of Science ®Google Scholar
• Patel VJ, Thalassinos K, Slade SE, et al. A comparison of labeling and label-free mass spectrometry-based proteomics approaches. J Proteome Res 2009;8:3752-9
   PubMed Web of Science ®Google Scholar
• Distler U, Kuharev J, Navarro P, et al. Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics. Nat Methods 2014;11:167-70
   PubMed Web of Science ®Google Scholar
• Geromanos SJ, Hughes C, Ciavarini S, et al. Using ion purity scores for enhancing quantitative accuracy and precision in complex proteomics samples. Anal Bioanal Chem 2012;404:1127-39
   PubMed Web of Science ®Google Scholar
• Valentine SJ, Liu X, Plasencia MD, et al. Developing liquid chromatography ion mobility mass spectometry techniques. Expert Rev Proteomics 2005;2:553-65
   PubMed Web of Science ®Google Scholar
• Zhong Y, Hyung S-J, Ruotolo BT. Ion mobility-mass spectrometry for structural proteomics. Expert Rev Proteomics 2012;9:47-58
   PubMed Web of Science ®Google Scholar
• Angel TE, Aryal UK, Hengel SM, et al. Mass spectrometry-based proteomics: existing capabilities and future directions. Chem Soc Rev 2012;41:3912-28
   PubMed Web of Science ®Google Scholar
• Lee S, Li Z, Valentine SJ, et al. Extracted Fragment Ion Mobility Distributions: a New Method for Complex Mixture Analysis. Int J Mass Spectrom 2012;309:154-60
   Google Scholar
• Valentine SJ, Ewing MA, Dilger JM, et al. Using ion mobility data to improve peptide identification: intrinsic amino acid size parameters. J Proteome Res 2011;10:2318-29
   Google Scholar
• Bond NJ, Shliaha P V, Lilley KS, Gatto L. Improving qualitative and quantitative performance for MS(E)-based label-free proteomics. J Proteome Res 2013;12:2340-53
   Google Scholar
• Valentine SJ, Plasencia MD, Liu X, et al. Toward plasma proteome profiling with ion mobility-mass spectrometry. J Proteome Res 2006;5:2977-84
   PubMed Web of Science ®Google Scholar
• Baker ES, Livesay EA, Orton DJ, et al. An LC-IMS-MS platform providing increased dynamic range for high-throughput proteomic studies. J Proteome Res 2010;9:997-1006
   PubMedGoogle Scholar
• Daly CE, Ng LL, Hakimi A, et al. Qualitative and quantitative characterization of plasma proteins when incorporating traveling wave ion mobility into a liquid chromatography-mass spectrometry workflow for biomarker discovery: use of product ion quantitation as an alternative data analysi. Anal Chem 2014;86:1972-9
   Google Scholar
• Foss EJ, Radulovic D, Stirewalt DL, et al. Proteomic classification of acute leukemias by alignment-based quantitation of LC-MS/MS data sets. J Proteome Res 2012;11:5005-10
   PubMed Web of Science ®Google Scholar
• Cox J, Hein MY, Luber CA, et al. MaxLFQ allows accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction. Mol Cell Proteomics 2014;13(9):2513-26
   PubMed Web of Science ®Google Scholar
• Zhang W, Zhang J, Xu C, et al. LFQuant: a label-free fast quantitative analysis tool for high-resolution LC-MS/MS proteomics data. Proteomics 2012;12:3475-84
   Google Scholar
• Benjamin AM, Thompson JW, Soderblom EJ, et al. A flexible statistical model for alignment of label-free proteomics data–incorporating ion mobility and product ion information. BMC Bioinformatics 2013;14:364
   Google Scholar
• Shliaha P V, Bond NJ, Gatto L, Lilley KS. Effects of traveling wave ion mobility separation on data independent acquisition in proteomics studies. J Proteome Res 2013;12:2323-39
   Google Scholar
• Cortes DF, Landis MK, Ottens AK. High-capacity peptide-centric platform to decode the proteomic response to brain injury. Electrophoresis 2012;33:3712-19
   PubMedGoogle Scholar
• Hoos MD, Richardson BM, Foster MW, et al. Longitudinal study of differential protein expression in an Alzheimer’s mouse model lacking inducible nitric oxide synthase. J Proteome Res 2013;12:4462-77
   Google Scholar
• Ottens AK, Stafflinger JE, Griffin HE, et al. Post-acute brain injury urinary signature: a new resource for molecular diagnostics. J Neurotrauma 2014;31:782-8
   PubMedGoogle Scholar
• Michel A, Schüler A, Friedrich P, et al. Mast cell-deficient Kit(W-sh) “Sash” mutant mice display aberrant myelopoiesis leading to the accumulation of splenocytes that act as myeloid-derived suppressor cells. J Immunol 2013;190:5534-44
   Google Scholar
• Alegre-Aguarón E, Sampat SR, Xiong JC, et al. Growth factor priming differentially modulates components of the extracellular matrix proteome in chondrocytes and synovium-derived stem cells. PLoS One 2014;9:e88053
   Google Scholar
• Parviainen VI, Joenväärä S, Tohmola N, Renkonen R. Label-free mass spectrometry proteome quantification of human embryonic kidney cells following 24 hours of sialic acid overproduction. Proteome Sci 2013;11:38
   Google Scholar
• Tenzer S, Moro A, Kuharev J, et al. Proteome-wide characterization of the RNA-binding protein RALY-interactome using the in vivo-biotinylation-pulldown-quant (iBioPQ) approach. J Proteome Res 2013;12:2869-84
   PubMed Web of Science ®Google Scholar
• Yang WS, SriRamaratnam R, Welsch ME, et al. Regulation of ferroptotic cancer cell death by GPX4. Cell 2014;156:317-31
   PubMed Web of Science ®Google Scholar
• Tenzer S, Docter D, Kuharev J, et al. Rapid formation of plasma protein corona critically affects nanoparticle pathophysiology. Nat Nanotechnol 2013;8:772-81
   PubMed Web of Science ®Google Scholar
• Helm S, Dobritzsch D, Rödiger A, et al. Protein identification and quantification by data-independent acquisition and multi-parallel collision-induced dissociation mass spectrometry (MS(E)) in the chloroplast stroma proteome. J Proteomics 2014;98:79-89
   Google Scholar
• Fan Y, Thompson JW, Dubois LG, et al. Proteomic analysis of an unculturable bacterial endosymbiont (Blochmannia) reveals high abundance of chaperonins and biosynthetic enzymes. J Proteome Res 2013;12:704-18
   PubMedGoogle Scholar
• Dator RP, Gaston KW, Limbach PA. Multiple enzymatic digestions and ion mobility separation improve quantification of bacterial ribosomal proteins by data independent acquisition liquid chromatography-mass spectrometry. Anal Chem 2014;86:4264-70
   Google Scholar
• Moran D, Cross T, Brown LM, et al. Data-independent acquisition (MSE) with ion mobility provides a systematic method for analysis of a bacteriophage structural proteome. J Virol Methods 2014;195:9-17
   Google Scholar
• Perrin RJ, Payton JE, Malone JP, et al. Quantitative label-free proteomics for discovery of biomarkers in cerebrospinal fluid: assessment of technical and inter-individual variation. PLoS One 2013;8:e64314
   PubMed Web of Science ®Google Scholar
• Piehowski PD, Petyuk VA, Orton DJ, et al. Sources of technical variability in quantitative LC-MS proteomics: human brain tissue sample analysis. J Proteome Res 2013;12:2128-37
   PubMed Web of Science ®Google Scholar
• Sandin M, Teleman J, Malmström J, Levander F. Data processing methods and quality control strategies for label-free LC-MS protein quantification. Biochim Biophys Acta 2014;1844:29-41
   PubMedGoogle Scholar
• Helm D, Vissers JP, Hughes CJ, et al. Ion mobility tandem mass spectrometry enhances performance of bottom-up proteomics. Mol Cell Proteomics 2014; [Epub ahead of print]
   Google Scholar
• Silveira JA, Ridgeway ME, Park MA. High resolution trapped ion mobility spectrometery of peptides. Anal Chem 2014;86:5624-7
   PubMed Web of Science ®Google Scholar
• Röst HL, Rosenberger G, Navarro P, et al. OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nat Biotechnol 2014;32:219-23
   PubMed Web of Science ®Google Scholar
• Liu S, Chen X, Yan Z, et al.et al. E) -based label-free proteomics and HRMS quantitation of small molecules. Proteomics 2014;14:169-80
   Google Scholar
• Pubmed. Available from: ncbi.nlm.nih.gov/entrez/query.fcgi
   Google Scholar