{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,6]],"date-time":"2025-11-06T11:42:57Z","timestamp":1762429377849,"version":"3.40.3"},"publisher-location":"New York, NY","reference-count":140,"publisher":"Springer New York","isbn-type":[{"type":"print","value":"9781493997435"},{"type":"electronic","value":"9781493997442"}],"license":[{"start":{"date-parts":[[2019,9,25]],"date-time":"2019-09-25T00:00:00Z","timestamp":1569369600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020]]},"DOI":"10.1007\/978-1-4939-9744-2_1","type":"book-chapter","created":{"date-parts":[[2019,9,24]],"date-time":"2019-09-24T17:04:34Z","timestamp":1569344674000},"page":"1-58","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Introduction to Mass Spectrometry-Based Proteomics"],"prefix":"10.1007","author":[{"given":"Rune","family":"Matthiesen","sequence":"first","affiliation":[]},{"given":"Jakob","family":"Bunkenborg","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2019,9,25]]},"reference":[{"issue":"20","key":"1_CR1","doi-asserted-by":"crossref","first-page":"4451","DOI":"10.1021\/j150664a002","volume":"88","author":"M Yamashita","year":"1984","unstructured":"Yamashita M, Fenn JB (1984) Electrospray ion source. Another variation on the free-jet theme. J Phys Chem 88(20):4451\u20134459","journal-title":"J Phys Chem"},{"issue":"20","key":"1_CR2","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1002\/rcm.1290020802","volume":"2","author":"K Tanaka","year":"1988","unstructured":"Tanaka K, Waki H, Ido Y, Akita S, Yoshida Y, Yoshida T, Matsuo T (1988) Protein and polymer analyses up to m\/z 100 000 by laser ionization time-of flight mass spectrometry. Rapid Commun Mass Spectrom 2(20):151\u2013153","journal-title":"Rapid Commun Mass Spectrom"},{"issue":"10","key":"1_CR3","doi-asserted-by":"crossref","first-page":"1791","DOI":"10.1002\/elps.11501601299","volume":"16","author":"SD Patterson","year":"1995","unstructured":"Patterson SD, Aebersold R (1995) Mass spectrometric approaches for the identification of gel-separated proteins. Electrophoresis 16(10):1791\u20131814","journal-title":"Electrophoresis"},{"issue":"4","key":"1_CR4","doi-asserted-by":"publisher","first-page":"430","DOI":"10.1002\/jms.856","volume":"40","author":"Q Hu","year":"2005","unstructured":"Hu Q, Noll RJ, Li H, Makarov A, Hardman M, Graham Cooks R (2005) The Orbitrap: a new mass spectrometer. J Mass Spectrom 40(4):430\u2013443. https:\/\/doi.org\/10.1002\/jms.856","journal-title":"J Mass Spectrom"},{"issue":"4926","key":"1_CR5","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1126\/science.2675315","volume":"246","author":"JB Fenn","year":"1989","unstructured":"Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246(4926):64\u201371","journal-title":"Science"},{"issue":"1","key":"1_CR6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1006\/abio.1996.9877","volume":"244","author":"KR Jonscher","year":"1997","unstructured":"Jonscher KR, Yates JR 3rd (1997) The quadrupole ion trap mass spectrometer\u2014a small solution to a big challenge. Anal Biochem 244(1):1\u201315. https:\/\/doi.org\/10.1006\/abio.1996.9877 . S0003-2697(96)99877-2","journal-title":"Anal Biochem"},{"key":"1_CR7","doi-asserted-by":"crossref","first-page":"4745","DOI":"10.1021\/ja01019a053","volume":"90","author":"WF Hadden","year":"1968","unstructured":"Hadden WF, McLafferty FW (1968) Metastable ion characteristics. VII. Collision-induced metastables. J Am Chem Soc 90:4745\u20134746","journal-title":"J Am Chem Soc"},{"key":"1_CR8","volume-title":"Mass spectrometry in biotechnology","author":"G Siuzak","year":"1996","unstructured":"Siuzak G (1996) Mass spectrometry in biotechnology. Academic Press, San Diego"},{"issue":"20","key":"1_CR9","doi-asserted-by":"crossref","first-page":"2299","DOI":"10.1021\/ac00171a028","volume":"60","author":"M Karas","year":"1988","unstructured":"Karas M, Hillenkamp F (1988) Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem 60(20):2299\u20132301","journal-title":"Anal Chem"},{"issue":"9","key":"1_CR10","doi-asserted-by":"publisher","first-page":"709","DOI":"10.1038\/nmeth1060","volume":"4","author":"JV Olsen","year":"2007","unstructured":"Olsen JV, Macek B, Lange O, Makarov A, Horning S, Mann M (2007) Higher-energy C-trap dissociation for peptide modification analysis. Nat Methods 4(9):709\u2013712. https:\/\/doi.org\/10.1038\/nmeth1060 . nmeth1060","journal-title":"Nat Methods"},{"issue":"3","key":"1_CR11","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1002\/mas.10041","volume":"22","author":"J Laskin","year":"2003","unstructured":"Laskin J, Futrell JH (2003) Collisional activation of peptide ions in FT-ICR mass spectrometry. Mass Spectrom Rev 22(3):158\u2013181. https:\/\/doi.org\/10.1002\/mas.10041","journal-title":"Mass Spectrom Rev"},{"issue":"3","key":"1_CR12","doi-asserted-by":"publisher","first-page":"764","DOI":"10.1006\/bbrc.1998.8466","volume":"245","author":"H Kuwata","year":"1998","unstructured":"Kuwata H, Yip TT, Yip CL, Tomita M, Hutchens TW (1998) Bactericidal domain of lactoferrin: detection, quantitation, and characterization of lactoferricin in serum by SELDI affinity mass spectrometry. Biochem Biophys Res Commun 245(3):764\u2013773. https:\/\/doi.org\/10.1006\/bbrc.1998.8466 . S0006-291X(98)98466-2","journal-title":"Biochem Biophys Res Commun"},{"issue":"26","key":"1_CR13","doi-asserted-by":"publisher","first-page":"9528","DOI":"10.1073\/pnas.0402700101","volume":"101","author":"JE Syka","year":"2004","unstructured":"Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF (2004) Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci U S A 101(26):9528\u20139533. https:\/\/doi.org\/10.1073\/pnas.0402700101 . 0402700101","journal-title":"Proc Natl Acad Sci U S A"},{"key":"1_CR14","doi-asserted-by":"crossref","first-page":"634R","DOI":"10.1021\/ac00084a024","volume":"66","author":"AL Burlingame","year":"1994","unstructured":"Burlingame AL, Boyd RK, Gaskell SJ (1994) Mass spectrometry. Anal Chem 66:634R\u2013683R","journal-title":"Anal Chem"},{"issue":"3","key":"1_CR15","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1021\/ac990811p","volume":"72","author":"RA Zubarev","year":"2000","unstructured":"Zubarev RA, Horn DM, Fridriksson EK, Kelleher NL, Kruger NA, Lewis MA, Carpenter BK, McLafferty FW (2000) Electron capture dissociation for structural characterization of multiply charged protein cations. Anal Chem 72(3):563\u2013573","journal-title":"Anal Chem"},{"key":"1_CR16","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.ijms.2004.08.004","volume":"238","author":"H James","year":"2004","unstructured":"James H, Barnes IV, Hieftje GM (2004) Recent advances in detector-array technology for mass spectrometry. Int J Mass Spectrom 238:33\u201346","journal-title":"Int J Mass Spectrom"},{"issue":"14","key":"1_CR17","doi-asserted-by":"publisher","first-page":"4050","DOI":"10.1021\/ac049848m","volume":"76","author":"Z Takats","year":"2004","unstructured":"Takats Z, Wiseman JM, Gologan B, Cooks RG (2004) Electrosonic spray ionization. A gentle technique for generating folded proteins and protein complexes in the gas phase and for studying ion-molecule reactions at atmospheric pressure. Anal Chem 76(14):4050\u20134058. https:\/\/doi.org\/10.1021\/ac049848m","journal-title":"Anal Chem"},{"issue":"191","key":"1_CR18","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/S1387-3806(99)00065-2","volume":"190","author":"JFJ Todd","year":"1999","unstructured":"Todd JFJ, March RE (1999) A retrospective review of the development and application of the quadrupole ion trap prior to the appearance of commercial instruments. Int J Mass Spectrom 190(191):9\u201335","journal-title":"Int J Mass Spectrom"},{"key":"1_CR19","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1002\/rcm.1290050412","volume":"5","author":"B Spengler","year":"1991","unstructured":"Spengler B, Kirsch D, Kaufmann R (1991) Metastable decay of peptides and proteins in matrix assisted laser desorption mass spectrometry. Rapid Commun Mass Spectrom 5:198\u2013202","journal-title":"Rapid Commun Mass Spectrom"},{"key":"1_CR20","first-page":"41","volume-title":"Gas phase ion chemistry","author":"LR Thorne","year":"1984","unstructured":"Thorne LR, Beauchamp JL (1984) In: Bowers MT (ed) Gas phase ion chemistry. Academic Press, London, p 41"},{"key":"1_CR21","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1007\/978-3-642-56895-4","volume-title":"Proteome research: mass spectrometry","author":"P James","year":"2001","unstructured":"James P (2001) Proteome research: mass spectrometry. Springer-Verlag, Berlin, Heidelberg, New York, p 35"},{"issue":"5","key":"1_CR22","doi-asserted-by":"publisher","first-page":"859","DOI":"10.1021\/ac951038a","volume":"68","author":"WD Price","year":"1996","unstructured":"Price WD, Schnier PD, Williams ER (1996) Tandem mass spectrometry of large biomolecule ions by blackbody infrared radiative dissociation. Anal Chem 68(5):859\u2013866. https:\/\/doi.org\/10.1021\/ac951038a","journal-title":"Anal Chem"},{"key":"1_CR23","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/j.aca.2003.12.031","volume":"509","author":"RR Barefoot","year":"2004","unstructured":"Barefoot RR (2004) Determination of platinum group elements and gold in geological materials: a review of recent magnetic sector and laser ablation applications. Anal Chim Acta 509:119\u2013125","journal-title":"Anal Chim Acta"},{"key":"1_CR24","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1016\/0020-7381(75)87033-1","volume":"16","author":"RG Cooks","year":"1975","unstructured":"Cooks RG, Ast T, Beynon JH (1975) Anomalous metastable peaks. Int J Mass Spectrom Ion Phys 16:55","journal-title":"Int J Mass Spectrom Ion Phys"},{"issue":"5796","key":"1_CR25","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1126\/science.1133987","volume":"314","author":"BT Chait","year":"2006","unstructured":"Chait BT (2006) Chemistry. Mass spectrometry: bottom-up or top-down? Science 314(5796):65\u201366. https:\/\/doi.org\/10.1126\/science.1133987 . 314\/5796\/65","journal-title":"Science"},{"issue":"8","key":"1_CR26","doi-asserted-by":"publisher","first-page":"822","DOI":"10.1038\/nmeth.2074","volume":"9","author":"C Wu","year":"2012","unstructured":"Wu C, Tran JC, Zamdborg L, Durbin KR, Li M, Ahlf DR, Early BP, Thomas PM, Sweedler JV, Kelleher NL (2012) A protease for \u2018middle-down\u2019 proteomics. Nat Methods 9(8):822\u2013824. https:\/\/doi.org\/10.1038\/nmeth.2074","journal-title":"Nat Methods"},{"issue":"11","key":"1_CR27","doi-asserted-by":"crossref","first-page":"197A","DOI":"10.1021\/ac0415657","volume":"76","author":"NL Kelleher","year":"2004","unstructured":"Kelleher NL (2004) Top-down proteomics. Anal Chem 76(11):197A\u2013203A","journal-title":"Anal Chem"},{"issue":"6","key":"1_CR28","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1002\/mas.20186","volume":"27","author":"RH Perry","year":"2008","unstructured":"Perry RH, Cooks RG, Noll RJ (2008) Orbitrap mass spectrometry: instrumentation, ion motion and applications. Mass Spectrom Rev 27(6):661\u2013699. https:\/\/doi.org\/10.1002\/mas.20186","journal-title":"Mass Spectrom Rev"},{"issue":"20","key":"1_CR29","doi-asserted-by":"publisher","first-page":"3566","DOI":"10.1002\/pmic.201000245","volume":"10","author":"A Armirotti","year":"2010","unstructured":"Armirotti A, Damonte G (2010) Achievements and perspectives of top-down proteomics. Proteomics 10(20):3566\u20133576. https:\/\/doi.org\/10.1002\/pmic.201000245","journal-title":"Proteomics"},{"issue":"3","key":"1_CR30","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1038\/85686","volume":"19","author":"MP Washburn","year":"2001","unstructured":"Washburn MP, Wolters D, Yates JR 3rd (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19(3):242\u2013247. https:\/\/doi.org\/10.1038\/85686 . 85686","journal-title":"Nat Biotechnol"},{"key":"1_CR31","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1007\/978-1-61779-148-2_18","volume":"753","author":"A Doucet","year":"2011","unstructured":"Doucet A, Kleifeld O, Kizhakkedathu JN, Overall CM (2011) Identification of proteolytic products and natural protein N-termini by Terminal Amine Isotopic Labeling of Substrates (TAILS). Methods Mol Biol 753:273\u2013287. https:\/\/doi.org\/10.1007\/978-1-61779-148-2_18","journal-title":"Methods Mol Biol"},{"key":"1_CR32","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1007\/978-1-61779-276-2_4","volume":"781","author":"O Schilling","year":"2011","unstructured":"Schilling O, Huesgen PF, Barre O, Overall CM (2011) Identification and relative quantification of native and proteolytically generated protein C-termini from complex proteomes: C-terminome analysis. Methods Mol Biol 781:59\u201369. https:\/\/doi.org\/10.1007\/978-1-61779-276-2_4","journal-title":"Methods Mol Biol"},{"issue":"5","key":"1_CR33","doi-asserted-by":"publisher","first-page":"894","DOI":"10.1074\/mcp.M000050-MCP201","volume":"9","author":"A Prudova","year":"2010","unstructured":"Prudova A, auf dem Keller U, Butler GS, Overall CM (2010) Multiplex N-terminome analysis of MMP-2 and MMP-9 substrate degradomes by iTRAQ-TAILS quantitative proteomics. Mol Cell Proteomics 9(5):894\u2013911. https:\/\/doi.org\/10.1074\/mcp.M000050-MCP201 . M000050-MCP201 [pii]","journal-title":"Mol Cell Proteomics"},{"issue":"10","key":"1_CR34","doi-asserted-by":"publisher","first-page":"771","DOI":"10.1038\/nmeth792","volume":"2","author":"P Damme Van","year":"2005","unstructured":"Van Damme P, Martens L, Van Damme J, Hugelier K, Staes A, Vandekerckhove J, Gevaert K (2005) Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis. Nat Methods 2(10):771\u2013777. https:\/\/doi.org\/10.1038\/nmeth792 . nmeth792 [pii]","journal-title":"Nat Methods"},{"issue":"1","key":"1_CR35","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1042\/BJ20070775","volume":"407","author":"JC Timmer","year":"2007","unstructured":"Timmer JC, Enoksson M, Wildfang E, Zhu W, Igarashi Y, Denault JB, Ma Y, Dummitt B, Chang YH, Mast AE, Eroshkin A, Smith JW, Tao WA, Salvesen GS (2007) Profiling constitutive proteolytic events in vivo. Biochem J 407(1):41\u201348. https:\/\/doi.org\/10.1042\/BJ20070775 . BJ20070775","journal-title":"Biochem J"},{"issue":"3","key":"1_CR36","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1586\/erm.11.12","volume":"11","author":"B Scola La","year":"2011","unstructured":"La Scola B (2011) Intact cell MALDI-TOF mass spectrometry-based approaches for the diagnosis of bloodstream infections. Expert Rev Mol Diagn 11(3):287\u2013298. https:\/\/doi.org\/10.1586\/erm.11.12","journal-title":"Expert Rev Mol Diagn"},{"issue":"18","key":"1_CR37","doi-asserted-by":"publisher","first-page":"7129","DOI":"10.1021\/ac201501z","volume":"83","author":"Q Zhang","year":"2011","unstructured":"Zhang Q, Willison LN, Tripathi P, Sathe SK, Roux KH, Emmett MR, Blakney GT, Zhang HM, Marshall AG (2011) Epitope mapping of a 95 kDa antigen in complex with antibody by solution-phase amide backbone hydrogen\/deuterium exchange monitored by Fourier transform ion cyclotron resonance mass spectrometry. Anal Chem 83(18):7129\u20137136. https:\/\/doi.org\/10.1021\/ac201501z","journal-title":"Anal Chem"},{"issue":"5185","key":"1_CR38","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1038\/2211056a0","volume":"221","author":"J Margolis","year":"1969","unstructured":"Margolis J, Kenrick KG (1969) 2-Dimensional resolution of plasma proteins by combination of polyacrylamide disc and gradient gel electrophoresis. Nature 221(5185):1056\u20131057","journal-title":"Nature"},{"issue":"6","key":"1_CR39","doi-asserted-by":"crossref","first-page":"1034","DOI":"10.1002\/elps.11501601175","volume":"16","author":"J Klose","year":"1995","unstructured":"Klose J, Kobalz U (1995) Two-dimensional electrophoresis of proteins: an updated protocol and implications for a functional analysis of the genome. Electrophoresis 16(6):1034\u20131059","journal-title":"Electrophoresis"},{"issue":"4","key":"1_CR40","doi-asserted-by":"publisher","first-page":"604","DOI":"10.1002\/pmic.201000404","volume":"11","author":"R Matthiesen","year":"2011","unstructured":"Matthiesen R, Azevedo L, Amorim A, Carvalho AS (2011) Discussion on common data analysis strategies used in MS-based proteomics. Proteomics 11(4):604\u2013619. https:\/\/doi.org\/10.1002\/pmic.201000404","journal-title":"Proteomics"},{"key":"1_CR41","doi-asserted-by":"crossref","first-page":"35","DOI":"10.2174\/1570164043488289","volume":"1","author":"N Inagaki","year":"2004","unstructured":"Inagaki N, Katsuta K (2004) Large gel two-dimensional electrophoresis: improving recovery of cellular proteome. Curr Proteomics 1:35\u201339","journal-title":"Curr Proteomics"},{"key":"1_CR42","doi-asserted-by":"crossref","first-page":"1720","DOI":"10.1128\/MCB.19.3.1720","volume":"19","author":"SP Gygi","year":"1999","unstructured":"Gygi SP, Rochon Y, Franza BR, Aebersold R (1999) Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19:1720\u20131730","journal-title":"Mol Cell Biol"},{"key":"1_CR43","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1016\/S0958-1669(02)00333-6","volume":"13","author":"WF Patton","year":"2002","unstructured":"Patton WF, Schulenberg B, Steinberg TH (2002) Two-dimensional gel electrophoresis; better than a poke in the ICAT? Curr Opin Biotechnol 13:321\u2013328","journal-title":"Curr Opin Biotechnol"},{"issue":"1","key":"1_CR44","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/0003-2697(92)90061-B","volume":"203","author":"J Rosenfeld","year":"1992","unstructured":"Rosenfeld J, Capdevielle J, Guillemot JC, Ferrara P (1992) In-gel digestion of proteins for internal sequence analysis after one- or two-dimensional gel electrophoresis. Anal Biochem 203(1):173\u2013179. 0003-2697(92)90061-B [pii]","journal-title":"Anal Biochem"},{"issue":"1","key":"1_CR45","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1006\/abio.1995.1070","volume":"224","author":"U Hellman","year":"1995","unstructured":"Hellman U, Wernstedt C, Gonez J, Heldin CH (1995) Improvement of an \u201cIn-Gel\u201d digestion procedure for the micropreparation of internal protein fragments for amino acid sequencing. Anal Biochem 224(1):451\u2013455. https:\/\/doi.org\/10.1006\/abio.1995.1070 . S0003-2697(85)71070-6 [pii]","journal-title":"Anal Biochem"},{"issue":"21","key":"1_CR46","doi-asserted-by":"crossref","first-page":"4800","DOI":"10.1021\/ac990448m","volume":"71","author":"WV Bienvenut","year":"1999","unstructured":"Bienvenut WV, Sanchez JC, Karmime A, Rouge V, Rose K, Binz PA, Hochstrasser DF (1999) Toward a clinical molecular scanner for proteome research: parallel protein chemical processing before and during western blot. Anal Chem 71(21):4800\u20134807","journal-title":"Anal Chem"},{"issue":"6928","key":"1_CR47","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1038\/nature01511","volume":"422","author":"R Aebersold","year":"2003","unstructured":"Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422(6928):198\u2013207. https:\/\/doi.org\/10.1038\/nature01511 . nature01511","journal-title":"Nature"},{"issue":"16","key":"1_CR48","doi-asserted-by":"publisher","first-page":"3040","DOI":"10.1002\/pmic.201000103","volume":"10","author":"J Bunkenborg","year":"2010","unstructured":"Bunkenborg J, Garcia GE, Paz MI, Andersen JS, Molina H (2010) The minotaur proteome: avoiding cross-species identifications deriving from bovine serum in cell culture models. Proteomics 10(16):3040\u20133044. https:\/\/doi.org\/10.1002\/pmic.201000103","journal-title":"Proteomics"},{"issue":"2","key":"1_CR49","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1016\/j.ab.2007.03.024","volume":"365","author":"C Zhao","year":"2007","unstructured":"Zhao C, O\u2019Connor PB (2007) Removal of polyethylene glycols from protein samples using titanium dioxide. Anal Biochem 365(2):283\u2013285. https:\/\/doi.org\/10.1016\/j.ab.2007.03.024 . S0003-2697(07)00185-6 [pii]","journal-title":"Anal Biochem"},{"key":"1_CR50","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.chroma.2004.07.110","volume":"1052","author":"S Williams","year":"2004","unstructured":"Williams S (2004) Ghost peaks in reversed-phase gradient HPLC: a review and update. J Chromatorgr A 1052:1\u201311","journal-title":"J Chromatorgr A"},{"issue":"12","key":"1_CR51","doi-asserted-by":"publisher","first-page":"5674","DOI":"10.1021\/pr900748n","volume":"8","author":"JR Wisniewski","year":"2009","unstructured":"Wisniewski JR, Zougman A, Mann M (2009) Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome. J Proteome Res 8(12):5674\u20135678. https:\/\/doi.org\/10.1021\/pr900748n","journal-title":"J Proteome Res"},{"key":"1_CR52","doi-asserted-by":"crossref","first-page":"6848","DOI":"10.1021\/ac049032l","volume":"76","author":"R Matthiesen","year":"2004","unstructured":"Matthiesen R, Bauw G, Welinder KG (2004) Use of performic acid oxidation to expand the mass distribution of tryptic peptides. Anal Chem 76:6848\u20136852","journal-title":"Anal Chem"},{"issue":"19","key":"1_CR53","doi-asserted-by":"publisher","first-page":"6426","DOI":"10.1021\/ac050923i","volume":"77","author":"M Gilar","year":"2005","unstructured":"Gilar M, Olivova P, Daly AE, Gebler JC (2005) Orthogonality of separation in two-dimensional liquid chromatography. Anal Chem 77(19):6426\u20136434. https:\/\/doi.org\/10.1021\/ac050923i","journal-title":"Anal Chem"},{"issue":"12","key":"1_CR54","doi-asserted-by":"publisher","first-page":"6176","DOI":"10.1021\/pr500893m","volume":"13","author":"TS Batth","year":"2014","unstructured":"Batth TS, Francavilla C, Olsen JV (2014) Off-line high-pH reversed-phase fractionation for in-depth phosphoproteomics. J Proteome Res 13(12):6176\u20136186. https:\/\/doi.org\/10.1021\/pr500893m","journal-title":"J Proteome Res"},{"issue":"8","key":"1_CR55","doi-asserted-by":"publisher","first-page":"3631","DOI":"10.1021\/pr4001465","volume":"12","author":"J Bunkenborg","year":"2013","unstructured":"Bunkenborg J, Espadas G, Molina H (2013) Cutting edge proteomics: benchmarking of six commercial trypsins. J Proteome Res 12(8):3631\u20133641. https:\/\/doi.org\/10.1021\/pr4001465","journal-title":"J Proteome Res"},{"issue":"17","key":"1_CR56","doi-asserted-by":"crossref","first-page":"4704","DOI":"10.1016\/S0021-9258(18)93681-1","volume":"244","author":"RL Smith","year":"1969","unstructured":"Smith RL, Shaw E (1969) Pseudotrypsin. A modified bovine trypsin produced by limited autodigestion. J Biol Chem 244(17):4704\u20134712","journal-title":"J Biol Chem"},{"key":"1_CR57","first-page":"531","volume":"112","author":"MR Wilkins","year":"1999","unstructured":"Wilkins MR, Gasteiger E, Bairoch A, Sanchez JC, Williams KL, Appel RD, Hochstrasser DF (1999) Protein identification and analysis tools in the ExPASy server. Methods Mol Biol 112:531\u2013552","journal-title":"Methods Mol Biol"},{"key":"1_CR58","unstructured":"S. G (2017) cleaver: cleavage of polypeptide sequences. R package version 1.18.0. https:\/\/github.com\/sgibb\/cleaver\/"},{"issue":"7","key":"1_CR59","doi-asserted-by":"crossref","first-page":"2172","DOI":"10.1021\/bi00007a010","volume":"34","author":"WS Willett","year":"1995","unstructured":"Willett WS, Gillmor SA, Perona JJ, Fletterick RJ, Craik CS (1995) Engineered metal regulation of trypsin specificity. Biochemistry 34(7):2172\u20132180","journal-title":"Biochemistry"},{"issue":"7376","key":"1_CR60","doi-asserted-by":"publisher","first-page":"254","DOI":"10.1038\/nature10575","volume":"480","author":"JC Tran","year":"2011","unstructured":"Tran JC, Zamdborg L, Ahlf DR, Lee JE, Catherman AD, Durbin KR, Tipton JD, Vellaichamy A, Kellie JF, Li M, Wu C, Sweet SM, Early BP, Siuti N, LeDuc RD, Compton PD, Thomas PM, Kelleher NL (2011) Mapping intact protein isoforms in discovery mode using top-down proteomics. Nature 480(7376):254\u2013258. https:\/\/doi.org\/10.1038\/nature10575 . nature10575","journal-title":"Nature"},{"key":"1_CR61","doi-asserted-by":"crossref","first-page":"1277","DOI":"10.1002\/1615-9861(200209)2:9<1277::AID-PROT1277>3.0.CO;2-P","volume":"2","author":"MR Larsen","year":"2002","unstructured":"Larsen MR, Cordwell SJ, Roepstorff P (2002) Graphite powder as an alternative or supplement to reversed-phase material for desalting and concentration of peptide mixtures prior to matrix-assisted laser desorption\/ionization-mass spectrometry. Proteomics 2:1277\u20131287","journal-title":"Proteomics"},{"issue":"3","key":"1_CR62","doi-asserted-by":"crossref","first-page":"556","DOI":"10.1021\/pr034112b","volume":"3","author":"P Hagglund","year":"2004","unstructured":"Hagglund P, Bunkenborg J, Elortza F, Jensen ON, Roepstorff P (2004) A new strategy for identification of N-glycosylated proteins and unambiguous assignment of their glycosylation sites using HILIC enrichment and partial deglycosylation. J Proteome Res 3(3):556\u2013566","journal-title":"J Proteome Res"},{"key":"1_CR63","doi-asserted-by":"crossref","first-page":"3935","DOI":"10.1021\/ac0498617","volume":"76","author":"MWH Pinkse","year":"2004","unstructured":"Pinkse MWH, Uitto PM, Hilhorst MJ, Ooms B, Heck AJR (2004) Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS\/MS and titanium oxide precolumns. Anal Chem 76:3935\u20133943","journal-title":"Anal Chem"},{"issue":"7","key":"1_CR64","doi-asserted-by":"publisher","first-page":"873","DOI":"10.1074\/mcp.T500007-MCP200","volume":"4","author":"MR Larsen","year":"2005","unstructured":"Larsen MR, Thingholm TE, Jensen ON, Roepstorff P, Jorgensen TJ (2005) Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol Cell Proteomics 4(7):873\u2013886. https:\/\/doi.org\/10.1074\/mcp.T500007-MCP200 . T500007-MCP200 [pii]","journal-title":"Mol Cell Proteomics"},{"issue":"12","key":"1_CR65","doi-asserted-by":"publisher","first-page":"6940","DOI":"10.1073\/pnas.0832254100","volume":"100","author":"SA Gerber","year":"2003","unstructured":"Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP (2003) Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci U S A 100(12):6940\u20136945. https:\/\/doi.org\/10.1073\/pnas.0832254100 . 0832254100","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"1_CR66","doi-asserted-by":"publisher","first-page":"1029","DOI":"10.1038\/nprot.2006.129","volume":"1","author":"JM Pratt","year":"2006","unstructured":"Pratt JM, Simpson DM, Doherty MK, Rivers J, Gaskell SJ, Beynon RJ (2006) Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Nat Protoc 1(2):1029\u20131043. https:\/\/doi.org\/10.1038\/nprot.2006.129 . nprot.2006.129 [pii]","journal-title":"Nat Protoc"},{"issue":"12","key":"1_CR67","doi-asserted-by":"publisher","first-page":"2139","DOI":"10.1074\/mcp.M700163-MCP200","volume":"6","author":"V Brun","year":"2007","unstructured":"Brun V, Dupuis A, Adrait A, Marcellin M, Thomas D, Court M, Vandenesch F, Garin J (2007) Isotope-labeled protein standards: toward absolute quantitative proteomics. Mol Cell Proteomics 6(12):2139\u20132149. https:\/\/doi.org\/10.1074\/mcp.M700163-MCP200 . M700163-MCP200 [pii]","journal-title":"Mol Cell Proteomics"},{"issue":"4","key":"1_CR68","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1016\/j.ymeth.2011.05.005","volume":"54","author":"P Brownridge","year":"2011","unstructured":"Brownridge P, Beynon RJ (2011) The importance of the digest: proteolysis and absolute quantification in proteomics. Methods 54(4):351\u2013360. https:\/\/doi.org\/10.1016\/j.ymeth.2011.05.005 . S1046-2023(11)00097-1","journal-title":"Methods"},{"issue":"6","key":"1_CR69","doi-asserted-by":"publisher","first-page":"F1799","DOI":"10.1152\/ajprenal.90510.2008","volume":"295","author":"AN Sachs","year":"2008","unstructured":"Sachs AN, Pisitkun T, Hoffert JD, Yu MJ, Knepper MA (2008) LC-MS\/MS analysis of differential centrifugation fractions from native inner medullary collecting duct of rat. Am J Physiol Renal Physiol 295(6):F1799\u2013F1806. https:\/\/doi.org\/10.1152\/ajprenal.90510.2008 . 90510.2008 [pii]","journal-title":"Am J Physiol Renal Physiol"},{"issue":"6","key":"1_CR70","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1080\/10611860600833955","volume":"14","author":"FP Seib","year":"2006","unstructured":"Seib FP, Jones AT, Duncan R (2006) Establishment of subcellular fractionation techniques to monitor the intracellular fate of polymer therapeutics I. Differential centrifugation fractionation B16F10 cells and use to study the intracellular fate of HPMA copolymer \u2013 doxorubicin. J Drug Target 14(6):375\u2013390. https:\/\/doi.org\/10.1080\/10611860600833955 . Q2801G62J27V1H10 [pii]","journal-title":"J Drug Target"},{"key":"1_CR71","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1007\/978-1-59745-353-0_2","volume":"370","author":"R Vogelmann","year":"2007","unstructured":"Vogelmann R, Nelson WJ (2007) Separation of cell-cell adhesion complexes by differential centrifugation. Methods Mol Biol 370:11\u201322. https:\/\/doi.org\/10.1007\/978-1-59745-353-0_2 . 1-59745-353-6:11 [pii]","journal-title":"Methods Mol Biol"},{"issue":"1","key":"1_CR72","doi-asserted-by":"publisher","first-page":"pdb.prot4309","DOI":"10.1101\/pdb.prot4309","volume":"2006","author":"Richard J. Simpson","year":"2006","unstructured":"Simpson RJ (2006) Fractional precipitation of proteins by ammonium sulfate. CSH Protoc 2006(1). https:\/\/doi.org\/10.1101\/pdb.prot4309 . 2006\/1\/pdb.prot4309","journal-title":"Cold Spring Harbor Protocols"},{"key":"1_CR73","doi-asserted-by":"publisher","unstructured":"Wingfield P (2001) Protein precipitation using ammonium sulfate. Curr Protoc Protein Sci Appendix 3:Appendix 3F. https:\/\/doi.org\/10.1002\/0471140864.psa03fs13","DOI":"10.1002\/0471140864.psa03fs13"},{"issue":"10","key":"1_CR74","doi-asserted-by":"publisher","first-page":"2998","DOI":"10.1016\/j.jprot.2011.12.001","volume":"75","author":"Fernando Lopitz-Otsoa","year":"2012","unstructured":"Lopitz-Otsoa F, Rodriguez-Suarez E, Aillet F, Casado-Vela J, Lang V, Matthiesen R, Elortza F, Rodriguez MS (2011) Integrative analysis of the ubiquitin proteome isolated using Tandem Ubiquitin Binding Entities (TUBEs). J Proteomics. https:\/\/doi.org\/10.1016\/j.jprot.2011.12.001 . S1874-3919(11)00668-3","journal-title":"Journal of Proteomics"},{"issue":"17","key":"1_CR75","doi-asserted-by":"publisher","first-page":"2957","DOI":"10.1002\/elps.200900064","volume":"30","author":"Z Dai","year":"2009","unstructured":"Dai Z, Zhou J, Qiu SJ, Liu YK, Fan J (2009) Lectin-based glycoproteomics to explore and analyze hepatocellular carcinoma-related glycoprotein markers. Electrophoresis 30(17):2957\u20132966. https:\/\/doi.org\/10.1002\/elps.200900064","journal-title":"Electrophoresis"},{"issue":"5","key":"1_CR76","doi-asserted-by":"publisher","first-page":"964","DOI":"10.1002\/pmic.201000429","volume":"11","author":"KY Fung","year":"2011","unstructured":"Fung KY, Cursaro C, Lewanowitsch T, Brierley GV, McColl SR, Lockett T, Head R, Hoffmann P, Cosgrove L (2011) A combined free-flow electrophoresis and DIGE approach to identify proteins regulated by butyrate in HT29 cells. Proteomics 11(5):964\u2013971. https:\/\/doi.org\/10.1002\/pmic.201000429","journal-title":"Proteomics"},{"issue":"8","key":"1_CR77","doi-asserted-by":"publisher","first-page":"2297","DOI":"10.1016\/j.jprot.2012.01.034","volume":"75","author":"Ki Hun Kim","year":"2012","unstructured":"Kim KH, Kim JY, Kim MO, Moon MH (2012) Two dimensional (pI & d(s)) separation of phosphorylated proteins by isoelectric focusing\/asymmetrical flow field-flow fractionation: Application to prostatic cancer cell line. J Proteomics. https:\/\/doi.org\/10.1016\/j.jprot.2012.01.034 . S1874-3919(12)00074-7","journal-title":"Journal of Proteomics"},{"key":"1_CR78","first-page":"156","volume":"27","author":"V B\u00f6kelmann","year":"1995","unstructured":"B\u00f6kelmann V, Spengler B, Kaufmann R (1995) Dynamical parameters of ion ejection and ion formation in matrix-assisted laser desorption\/ionization. Eur Mass Spectrom 27:156\u2013158","journal-title":"Eur Mass Spectrom"},{"issue":"17","key":"1_CR79","doi-asserted-by":"crossref","first-page":"6873","DOI":"10.1073\/pnas.87.17.6873","volume":"87","author":"RC Beavis","year":"1990","unstructured":"Beavis RC, Chait BT (1990) Rapid, sensitive analysis of protein mixtures by mass spectrometry. Proc Natl Acad Sci U S A 87(17):6873\u20136877","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"1_CR80","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1021\/ac9507956","volume":"68","author":"SL Cohen","year":"1996","unstructured":"Cohen SL, Chait BT (1996) Influence of matrix solution conditions on the MALDI-MS analysis of peptides and proteins. Anal Chem 68(1):31\u201337","journal-title":"Anal Chem"},{"key":"1_CR81","doi-asserted-by":"crossref","first-page":"3281","DOI":"10.1021\/ac00091a044","volume":"66","author":"O Vorm","year":"1994","unstructured":"Vorm O, Roepstorff P, Mann M (1994) Improved resolution and very high sensitivity in MALDI TOF of matrix surfaces made by fast evaporation. Anal Chem 66:3281\u20133287","journal-title":"Anal Chem"},{"key":"1_CR82","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1002\/(SICI)1096-9888(199706)32:6<593::AID-JMS511>3.0.CO;2-D","volume":"32","author":"M Kussmann","year":"1997","unstructured":"Kussmann M, Nordhoff E, Nielsen RB, H\u00e1bel S, Larsen MR, Jakobsen L, Gobom J, Mirgorodskaya E, Kristensen AK, Palm L, Roepstorff P (1997) Matrix-assisted laser desorption\/ionization mass spectrometry sample preparation techniques designed for various peptide and protein analytes. J Mass Spectrom 32:593\u2013601","journal-title":"J Mass Spectrom"},{"key":"1_CR83","doi-asserted-by":"crossref","first-page":"1519","DOI":"10.1002\/jms.1190301102","volume":"30","author":"M Guilhaus","year":"1995","unstructured":"Guilhaus M (1995) Principles and instrumentation in time-of-flight mass spectrometry. J Mass Spectrom 30:1519\u20131552","journal-title":"J Mass Spectrom"},{"issue":"16","key":"1_CR84","doi-asserted-by":"publisher","first-page":"2815","DOI":"10.1002\/pmic.200700116","volume":"7","author":"R Matthiesen","year":"2007","unstructured":"Matthiesen R (2007) Methods, algorithms and tools in computational proteomics: a practical point of view. Proteomics 7(16):2815\u20132832. https:\/\/doi.org\/10.1002\/pmic.200700116","journal-title":"Proteomics"},{"key":"1_CR85","doi-asserted-by":"crossref","first-page":"1044","DOI":"10.1002\/rcm.1290091115","volume":"9","author":"ML Vestal","year":"1995","unstructured":"Vestal ML, Juhasz P, Martin SA (1995) Delayed extraction matrix-assisted laser desorption time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 9:1044\u20131050","journal-title":"Rapid Commun Mass Spectrom"},{"issue":"7","key":"1_CR86","doi-asserted-by":"crossref","first-page":"1104","DOI":"10.1002\/elps.11501601187","volume":"16","author":"SD Patterson","year":"1995","unstructured":"Patterson SD (1995) Matrix-assisted laser-desorption\/ionization mass spectrometric approaches for the identification of gel-separated proteins in the 5\u201350 pmol range. Electrophoresis 16(7):1104\u20131114","journal-title":"Electrophoresis"},{"key":"1_CR87","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/S1044-0305(99)00126-9","volume":"11","author":"BO Keller","year":"2000","unstructured":"Keller BO, Li L (2000) Discerning matrix-cluster peaks in matrix-assisted laser desorption\/ionization time-of-flight mass spectra of dilute peptide mixtures. J Am Soc Mass Spectrom 11:88\u201393","journal-title":"J Am Soc Mass Spectrom"},{"key":"1_CR88","doi-asserted-by":"crossref","first-page":"1637","DOI":"10.1021\/ac010979m","volume":"74","author":"Z Guo","year":"2002","unstructured":"Guo Z, Zhang Q, Zou H, Guo B, Ni J (2002) A method for the analysis of low-mass molecules by MALDI-TOF mass spectrometry. Anal Chem 74:1637\u20131641","journal-title":"Anal Chem"},{"key":"1_CR89","unstructured":"Coursey JS, Schwab DJ, Dragoset RA (2001) Atomic weights and isotopic compositions (version 2.3.1). Available: http:\/\/physics.nist.gov\/Comp . 7 July 2003. National Institute of Standards and Technology, Gaithersburg, MD"},{"key":"1_CR90","volume-title":"Interpreting protein mass spectra, a comprehensive resource","author":"AP Snyder","year":"2000","unstructured":"Snyder AP (2000) Interpreting protein mass spectra, a comprehensive resource. Oxford University Press, Oxford"},{"key":"1_CR91","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1093\/jnen\/62.8.855","volume":"62","author":"PP Zheng","year":"2003","unstructured":"Zheng PP, Luider TM, Pieters R, Avezaat CJ, van den Bent MJ, Smitt SPA, Kros JM (2003) Identification of tumor-related proteins by proteomic analysis of cerebrospinal fluid from patients with primary brain tumors. J Neuropathol Exp Neurol 62:855\u2013862","journal-title":"J Neuropathol Exp Neurol"},{"issue":"23","key":"1_CR92","doi-asserted-by":"crossref","first-page":"4741","DOI":"10.1021\/ac970896z","volume":"69","author":"ON Jensen","year":"1997","unstructured":"Jensen ON, Podtelejnikov AV, Mann M (1997) Identification of the components of simple protein mixtures by high-accuracy peptide mass mapping and database searching. Anal Chem 69(23):4741\u20134750","journal-title":"Anal Chem"},{"key":"1_CR93","doi-asserted-by":"crossref","first-page":"1406","DOI":"10.1002\/1615-9861(200210)2:10<1406::AID-PROT1406>3.0.CO;2-9","volume":"2","author":"N Zhang","year":"2002","unstructured":"Zhang N, Aebersold R, Schwikowski B (2002) ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data. Proteomics 2:1406\u20131412","journal-title":"Proteomics"},{"issue":"9","key":"1_CR94","doi-asserted-by":"crossref","first-page":"882","DOI":"10.1021\/ac00208a002","volume":"62","author":"RD Smith","year":"1990","unstructured":"Smith RD, Loo JA, Edmonds CG, Barinaga CJ, Udseth HR (1990) New developments in biochemical mass spectrometry: electrospray ionization. Anal Chem 62(9):882\u2013899","journal-title":"Anal Chem"},{"key":"1_CR95","doi-asserted-by":"crossref","first-page":"1989","DOI":"10.1021\/ac00018a017","volume":"63","author":"MG Ikonomou","year":"1991","unstructured":"Ikonomou MG, Blades AT, Kebarle P (1991) Electrospray-ion spray: a comparison of mechanisms and performance. Anal Chem 63:1989\u20131998","journal-title":"Anal Chem"},{"key":"1_CR96","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1002\/rcm.1290021111","volume":"2","author":"TR Covey","year":"1988","unstructured":"Covey TR, Bonner RF, Shushan BI, Henion J (1988) The determination of protein, oligonucleotide and peptide molecular weights by ion-spray mass spectrometry. Rapid Commun Mass Spectrom 2:249\u2013256","journal-title":"Rapid Commun Mass Spectrom"},{"issue":"18","key":"1_CR97","doi-asserted-by":"crossref","first-page":"2898","DOI":"10.1021\/ac00090a017","volume":"66","author":"UA Mirza","year":"1994","unstructured":"Mirza UA, Chait BT (1994) Effects of anions on the positive ion electrospray ionization mass spectra of peptides and proteins. Anal Chem 66(18):2898\u20132904","journal-title":"Anal Chem"},{"key":"1_CR98","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1002\/jms.422","volume":"38","author":"T K\u00f6cher","year":"2003","unstructured":"K\u00f6cher T, Allmaier G, Wilm M (2003) Nanoelectrospray-based detection and sequencing of substoichiometric amounts of phosphopeptides in complex mixtures. J Mass Spectrom 38:131\u2013137","journal-title":"J Mass Spectrom"},{"key":"1_CR99","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1021\/ac00077a021","volume":"66","author":"CL Gatlin","year":"1994","unstructured":"Gatlin CL, Ture\u00e7ek F (1994) Acidity determination in droplets formed by electrospraying methanol-water solutions. Anal Chem 66:712\u2013718","journal-title":"Anal Chem"},{"issue":"1","key":"1_CR100","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1021\/ac9509519","volume":"68","author":"M Wilm","year":"1996","unstructured":"Wilm M, Mann M (1996) Analytical properties of the nanoelectrospray ion source. Anal Chem 68(1):1\u20138","journal-title":"Anal Chem"},{"key":"1_CR101","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/S0021-9673(00)00530-6","volume":"887","author":"G Choudhary","year":"2000","unstructured":"Choudhary G, Apffel A, Yin H, Hancock W (2000) Use of on-line mass spectrometric detection in capillary electrochromatography. J Chromatogr A 887:85\u2013101","journal-title":"J Chromatogr A"},{"key":"1_CR102","doi-asserted-by":"crossref","first-page":"1889","DOI":"10.1002\/rcm.1130","volume":"17","author":"A Urvoas","year":"2003","unstructured":"Urvoas A, Amekraz B, Moulin C, Clainche LL, Stocklin R, Moutiez M (2003) Analysis of the metal-binding selectivity of the metallochaperone CopZ from Enterococcus hirae by electrospray ionization mass spectrometry. Rapid Commun Mass Spectrom 17:1889\u20131896","journal-title":"Rapid Commun Mass Spectrom"},{"issue":"6564","key":"1_CR103","doi-asserted-by":"publisher","first-page":"466","DOI":"10.1038\/379466a0","volume":"379","author":"M Wilm","year":"1996","unstructured":"Wilm M, Shevchenko A, Houthaeve T, Breit S, Schweigerer L, Fotsis T, Mann M (1996) Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature 379(6564):466\u2013469. https:\/\/doi.org\/10.1038\/379466a0","journal-title":"Nature"},{"key":"1_CR104","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1002\/jms.207","volume":"36","author":"IV Chernushevich","year":"2001","unstructured":"Chernushevich IV, Loboda AV, Thomson BA (2001) An introduction to quadrupole\u2013time-of-flight mass spectrometry. J Mass Spectrom 36:849\u2013865","journal-title":"J Mass Spectrom"},{"issue":"7","key":"1_CR105","doi-asserted-by":"publisher","first-page":"916","DOI":"10.1016\/j.jasms.2006.02.009","volume":"17","author":"SA Lammert","year":"2006","unstructured":"Lammert SA, Rockwood AA, Wang M, Lee ML, Lee ED, Tolley SE, Oliphant JR, Jones JL, Waite RW (2006) Miniature toroidal radio frequency ion trap mass analyzer. J Am Soc Mass Spectrom 17(7):916\u2013922. https:\/\/doi.org\/10.1016\/j.jasms.2006.02.009 . S1044-0305(06)00125-5","journal-title":"J Am Soc Mass Spectrom"},{"issue":"9","key":"1_CR106","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M111.011015","volume":"10","author":"A Michalski","year":"2011","unstructured":"Michalski A, Damoc E, Hauschild JP, Lange O, Wieghaus A, Makarov A, Nagaraj N, Cox J, Mann M, Horning S (2011) Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol Cell Proteomics 10(9):M111.011015. https:\/\/doi.org\/10.1074\/mcp.M111.011015","journal-title":"Mol Cell Proteomics"},{"issue":"8","key":"1_CR107","doi-asserted-by":"publisher","first-page":"3021","DOI":"10.1021\/pr0700605","volume":"6","author":"P Hagglund","year":"2007","unstructured":"Hagglund P, Matthiesen R, Elortza F, Hojrup P, Roepstorff P, Jensen ON, Bunkenborg J (2007) An enzymatic deglycosylation scheme enabling identification of core fucosylated N-glycans and O-glycosylation site mapping of human plasma proteins. J Proteome Res 6(8):3021\u20133031. https:\/\/doi.org\/10.1021\/pr0700605","journal-title":"J Proteome Res"},{"issue":"2","key":"1_CR108","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1006\/abio.1996.0313","volume":"239","author":"SA Carr","year":"1996","unstructured":"Carr SA, Huddleston MJ, Annan RS (1996) Selective detection and sequencing of phosphopeptides at the femtomole level by mass spectrometry. Anal Biochem 239(2):180\u2013192. https:\/\/doi.org\/10.1006\/abio.1996.0313 . S0003-2697(96)90313-9","journal-title":"Anal Biochem"},{"issue":"6","key":"1_CR109","doi-asserted-by":"publisher","first-page":"1106","DOI":"10.1002\/pmic.200900396","volume":"10","author":"JA Cham Mead","year":"2010","unstructured":"Cham Mead JA, Bianco L, Bessant C (2010) Free computational resources for designing selected reaction monitoring transitions. Proteomics 10(6):1106\u20131126. https:\/\/doi.org\/10.1002\/pmic.200900396","journal-title":"Proteomics"},{"issue":"5","key":"1_CR110","doi-asserted-by":"publisher","first-page":"1120","DOI":"10.1002\/pmic.200800577","volume":"9","author":"J Sherman","year":"2009","unstructured":"Sherman J, McKay MJ, Ashman K, Molloy MP (2009) How specific is my SRM?: the issue of precursor and product ion redundancy. Proteomics 9(5):1120\u20131123. https:\/\/doi.org\/10.1002\/pmic.200800577","journal-title":"Proteomics"},{"key":"1_CR111","doi-asserted-by":"crossref","DOI":"10.1002\/0471721980","volume-title":"Protein sequencing and identification using tandem mass spectrometry","author":"M Kinter","year":"2000","unstructured":"Kinter M, Sherman NE (2000) Protein sequencing and identification using tandem mass spectrometry. John Wiley & Sons, New York"},{"issue":"10","key":"1_CR112","doi-asserted-by":"publisher","first-page":"1426","DOI":"10.1002\/1615-9861(200210)2:10<1426::AID-PROT1426>3.0.CO;2-5","volume":"2","author":"DM Creasy","year":"2002","unstructured":"Creasy DM, Cottrell JS (2002) Error tolerant searching of uninterpreted tandem mass spectrometry data. Proteomics 2(10):1426\u20131434. https:\/\/doi.org\/10.1002\/1615-9861(200210)2:10<1426::AID-PROT1426>3.0.CO;2-5","journal-title":"Proteomics"},{"issue":"11","key":"1_CR113","doi-asserted-by":"crossref","first-page":"976","DOI":"10.1016\/1044-0305(94)80016-2","volume":"5","author":"J Eng","year":"1994","unstructured":"Eng J, McCormack A, Yates J (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5(11):976\u2013989","journal-title":"J Am Soc Mass Spectrom"},{"issue":"8","key":"1_CR114","doi-asserted-by":"publisher","first-page":"1454","DOI":"10.1002\/pmic.200300485","volume":"3","author":"J Colinge","year":"2003","unstructured":"Colinge J, Masselot A, Giron M, Dessingy T, Magnin J (2003) OLAV: towards high-throughput tandem mass spectrometry data identification. Proteomics 3(8):1454\u20131463. https:\/\/doi.org\/10.1002\/pmic.200300485","journal-title":"Proteomics"},{"key":"1_CR115","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1385\/1-59745-275-0:121","volume":"367","author":"R Matthiesen","year":"2007","unstructured":"Matthiesen R (2007) Virtual Expert Mass Spectrometrist v3.0: an integrated tool for proteome analysis. Methods Mol Biol 367:121\u2013138. https:\/\/doi.org\/10.1385\/1-59745-275-0:121","journal-title":"Methods Mol Biol"},{"issue":"1","key":"1_CR116","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1021\/pr0701198","volume":"7","author":"RD Bjornson","year":"2008","unstructured":"Bjornson RD, Carriero NJ, Colangelo C, Shifman M, Cheung KH, Miller PL, Williams K (2008) X!!Tandem, an improved method for running X!tandem in parallel on collections of commodity computers. J Proteome Res 7(1):293\u2013299. https:\/\/doi.org\/10.1021\/pr0701198","journal-title":"J Proteome Res"},{"issue":"4","key":"1_CR117","doi-asserted-by":"publisher","first-page":"1794","DOI":"10.1021\/pr101065j","volume":"10","author":"J Cox","year":"2011","unstructured":"Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M (2011) Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res 10(4):1794\u20131805. https:\/\/doi.org\/10.1021\/pr101065j","journal-title":"J Proteome Res"},{"issue":"12","key":"1_CR118","doi-asserted-by":"publisher","first-page":"2376","DOI":"10.1002\/pmic.200701126","volume":"8","author":"R Tharakan","year":"2008","unstructured":"Tharakan R, Martens L, Van Eyk JE, Graham DR (2008) OMSSAGUI: an open-source user interface component to configure and run the OMSSA search engine. Proteomics 8(12):2376\u20132378. https:\/\/doi.org\/10.1002\/pmic.200701126","journal-title":"Proteomics"},{"key":"1_CR119","doi-asserted-by":"crossref","first-page":"1399","DOI":"10.1002\/1096-9888(200012)35:12<1399::AID-JMS86>3.0.CO;2-R","volume":"35","author":"VH Wysocki","year":"2000","unstructured":"Wysocki VH, Tsaprailis G, Smith LL, Breci LA (2000) Mobile and localized protons: a framework for understanding peptide dissociation. J Mass Spectrom 35:1399\u20131406","journal-title":"J Mass Spectrom"},{"key":"1_CR120","doi-asserted-by":"crossref","first-page":"1699","DOI":"10.1002\/rcm.747","volume":"16","author":"B Paizs","year":"2002","unstructured":"Paizs B, Suhai S (2002) Towards understanding some ion intensity relationships for the tandem mass spectra of protonated peptides. Rapid Commun Mass Spectrom 16:1699\u20131702","journal-title":"Rapid Commun Mass Spectrom"},{"issue":"11","key":"1_CR121","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1002\/bms.1200111109","volume":"11","author":"P Roepstorff","year":"1984","unstructured":"Roepstorff P, Fohlman J (1984) Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed Mass Spectrom 11(11):601. https:\/\/doi.org\/10.1002\/bms.1200111109","journal-title":"Biomed Mass Spectrom"},{"issue":"3","key":"1_CR122","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1021\/ac0258913","volume":"75","author":"M Havilio","year":"2003","unstructured":"Havilio M, Haddad Y, Smilansky Z (2003) Intensity-based statistical scorer for tandem mass spectrometry. Anal Chem 75(3):435\u2013444","journal-title":"Anal Chem"},{"key":"1_CR123","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1002\/(SICI)1096-9888(199702)32:2<225::AID-JMS471>3.0.CO;2-#","volume":"32","author":"SG Summerfield","year":"1997","unstructured":"Summerfield SG, Bolgar MS, Gaskell SJ (1997) Promotion and stabilization of ions in peptide b1 phenythiocarbamoyl derivatives: analogies with condensed-phase chemistry. J Mass Spectrom 32:225\u2013231","journal-title":"J Mass Spectrom"},{"issue":"5","key":"1_CR124","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1002\/1615-9861(200205)2:5<524::AID-PROT524>3.0.CO;2-O","volume":"2","author":"A Schlosser","year":"2002","unstructured":"Schlosser A, Lehmann WD (2002) Patchwork peptide sequencing: extraction of sequence information from accurate mass data of peptide tandem mass spectra recorded at high resolution. Proteomics 2(5):524\u2013533. https:\/\/doi.org\/10.1002\/1615-9861(200205)2:5<524::AID-PROT524>3.0.CO;2-O","journal-title":"Proteomics"},{"key":"1_CR125","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1002\/1096-9888(200006)35:6<683::AID-JMS994>3.0.CO;2-D","volume":"35","author":"AG Harrison","year":"2000","unstructured":"Harrison AG, Csizmadia IG, Tang TH, Tu YP (2000) Reaction competition in the fragmentation of protonated dipeptides. J Mass Spectrom 35:683\u2013688","journal-title":"J Mass Spectrom"},{"issue":"10","key":"1_CR126","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1002\/jms.703","volume":"39","author":"L Sleno","year":"2004","unstructured":"Sleno L, Volmer DA (2004) Ion activation methods for tandem mass spectrometry. J Mass Spectrom 39(10):1091\u20131112. https:\/\/doi.org\/10.1002\/jms.703","journal-title":"J Mass Spectrom"},{"issue":"6","key":"1_CR127","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1002\/(SICI)1097-0231(20000331)14:6<417::AID-RCM885>3.0.CO;2-J","volume":"14","author":"IP Csonka","year":"2000","unstructured":"Csonka IP, Paizs B, Lendvay G, Suhai S (2000) Proton mobility in protonated peptides: a joint molecular orbital and RRKM study. Rapid Commun Mass Spectrom 14(6):417\u2013431. https:\/\/doi.org\/10.1002\/(SICI)1097-0231(20000331)14:6<417::AID-RCM885>3.0.CO;2-J","journal-title":"Rapid Commun Mass Spectrom"},{"key":"1_CR128","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1002\/rcm.1290070908","volume":"7","author":"SA Lee","year":"1993","unstructured":"Lee SA, Jiao CQ, Huang Y, Freiser BS (1993) Multiple excitation collisional activation in Fourier-transform mass spectrometry. Rapid Commun Mass Spectrom 7:819\u2013821","journal-title":"Rapid Commun Mass Spectrom"},{"issue":"12","key":"1_CR129","doi-asserted-by":"publisher","first-page":"M111.009910","DOI":"10.1074\/mcp.M111.009910","volume":"10","author":"Mark P. Jedrychowski","year":"2011","unstructured":"Jedrychowski MP, Huttlin EL, Haas W, Sowa ME, Rad R, Gygi SP Evaluation of HCD- and CID-type fragmentation within their respective detection platforms for murine phosphoproteomics. Mol Cell Proteomics 10(12). https:\/\/doi.org\/10.1074\/mcp.M111.009910 . M111.009910 [pii]","journal-title":"Molecular & Cellular Proteomics"},{"key":"1_CR130","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/S1044-0305(01)00357-9","volume":"13","author":"HJ Cooper","year":"2002","unstructured":"Cooper HJ, Hudgins RR, H\u00e5kansson K, Marshall AG (2002) Characterization of amino acid side chain losses in electron capture dissociation. J Am Soc Mass Spectrom 13:241\u2013249","journal-title":"J Am Soc Mass Spectrom"},{"key":"1_CR131","doi-asserted-by":"crossref","first-page":"2857","DOI":"10.1021\/ja981948k","volume":"121","author":"RA Zubarev","year":"1999","unstructured":"Zubarev RA, Kruger NA, Fridriksson EK, Lewis MA, Horn DM, Carpenter BK, McLafferty FW (1999) Electron capture dissociation of gaseous multiply-charged proteins is favoured at disulphide bonds and other sites of high hydrogen atom affinity. J Am Chem Soc 121:2857\u20132862","journal-title":"J Am Chem Soc"},{"key":"1_CR132","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.bbrc.2005.05.138","volume":"334","author":"R Bakhtiar","year":"2005","unstructured":"Bakhtiar R, Guan Z (2005) Electron capture dissociation mass spectrometry in characterization of post-translational modifications. Biochem Biophys Res Commun 334:1\u20138","journal-title":"Biochem Biophys Res Commun"},{"issue":"11","key":"1_CR133","doi-asserted-by":"publisher","first-page":"1789","DOI":"10.1002\/pmic.201400186","volume":"15","author":"AS Carvalho","year":"2015","unstructured":"Carvalho AS, Penque D, Matthiesen R (2015) Bottom up proteomics data analysis strategies to explore protein modifications and genomic variants. Proteomics 15(11):1789\u20131792. https:\/\/doi.org\/10.1002\/pmic.201400186","journal-title":"Proteomics"},{"key":"1_CR134","doi-asserted-by":"crossref","first-page":"1793","DOI":"10.1002\/rcm.1119","volume":"17","author":"WR Cannon","year":"2003","unstructured":"Cannon WR, Jarman KD (2003) Improved peptide sequencing using isotope information inherent in tandem mass spectra. Rapid Commun Mass Spectrom 17:1793\u20131801","journal-title":"Rapid Commun Mass Spectrom"},{"key":"1_CR135","doi-asserted-by":"crossref","unstructured":"Cooks RG, Rockwood AL (1991) Rapid Commun Mass Spectrom 5, 93","DOI":"10.1002\/rcm.1290051203"},{"issue":"3","key":"1_CR136","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1016\/1044-0305(95)00675-3","volume":"7","author":"M Busman","year":"1996","unstructured":"Busman M, Schey KL, Oatis JE, Knapp DR (1996) Identification of phosphorylation sites in phosphopeptides by positive and negative mode electrospray ionization-tandem mass spectrometry. J Am Soc Mass Spectrom 7(3):243\u2013249. https:\/\/doi.org\/10.1016\/1044-0305(95)00675-3","journal-title":"J Am Soc Mass Spectrom"},{"issue":"1","key":"1_CR137","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1038\/nmeth705","volume":"1","author":"JD Venable","year":"2004","unstructured":"Venable JD, Dong MQ, Wohlschlegel J, Dillin A, Yates JR (2004) Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat Methods 1(1):39\u201345. https:\/\/doi.org\/10.1038\/nmeth705","journal-title":"Nat Methods"},{"issue":"13","key":"1_CR138","doi-asserted-by":"crossref","first-page":"1989","DOI":"10.1002\/rcm.2550","volume":"20","author":"RS Plumb","year":"2006","unstructured":"Plumb RS, Johnson KA, Rainville P, Smith BW, Wilson ID, Castro-Perez JM, Nicholson JK (2006) UPLC\/MSE; a new approach for generating molecular fragment information for biomarker structure elucidation. Rapid Commun Mass Spectrom 20(13):1989\u20131994","journal-title":"Rapid Commun Mass Spectrom"},{"issue":"15\u201316","key":"1_CR139","doi-asserted-by":"publisher","first-page":"2065","DOI":"10.1002\/pmic.201600203","volume":"16","author":"R Aebersold","year":"2016","unstructured":"Aebersold R, Bensimon A, Collins BC, Ludwig C, Sabido E (2016) Applications and developments in targeted proteomics: from SRM to DIA\/SWATH. Proteomics 16(15\u201316):2065\u20132067. https:\/\/doi.org\/10.1002\/pmic.201600203","journal-title":"Proteomics"},{"key":"1_CR140","unstructured":"Lide DR (1992\u20131993) Handbook of chemistry and physics, CRC Press, 73rd edn, p 11.2"}],"container-title":["Methods in Molecular Biology","Mass Spectrometry Data Analysis in Proteomics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-1-4939-9744-2_1","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,1,23]],"date-time":"2021-01-23T01:35:46Z","timestamp":1611365746000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-1-4939-9744-2_1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,9,25]]},"ISBN":["9781493997435","9781493997442"],"references-count":140,"URL":"https:\/\/doi.org\/10.1007\/978-1-4939-9744-2_1","relation":{},"ISSN":["1064-3745","1940-6029"],"issn-type":[{"type":"print","value":"1064-3745"},{"type":"electronic","value":"1940-6029"}],"subject":[],"published":{"date-parts":[[2019,9,25]]},"assertion":[{"value":"25 September 2019","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}}]}}