Smith LM, Kelleher NL, Linial M, Goodlett D, Langridge-Smith P, Ah Goo Y, Safford G, Bonilla* L, Kruppa G, Zubarev R, Rontree J, Chamot-Rooke J, Garavelli J, Heck A, Loo J, Penque D, Hornshaw M, Hendrickson C, Pasa-Tolic L, Borchers C, Chan D, Young* N, Agar J, Masselon C, Gross* M, McLafferty F, Tsybin Y, Ge Y, Sanders* I, Langridge J, Whitelegge* J, Marshall A. The consortium for top down, P., proteoform: a single term describing protein complexity. Nat Methods. 2013;10(3):186–7.

Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlén M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA; Young, N. L.;, Zhang. B., How many human proteoforms are there? Nat Chem Biol 2018, 14 (3), 206–214.

Smith LM, Agar JN, Chamot-Rooke J, Danis PO, Ge Y, Loo JA, Paša-Tolić L, Tsybin YO, Kelleher NL. The human proteoform project: defining the human proteome. Sci Adv. 2021;7(46):eabk0734.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Picotti P, Clément-Ziza M, Lam H, Campbell DS, Schmidt A, Deutsch EW, Röst H, Sun Z, Rinner O, Reiter L, Shen Q, Michaelson JJ, Frei A, Alberti S, Kusebauch U, Wollscheid B, Moritz RL, Beyer A, Aebersold R. A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature. 2013;494(7436):266–70.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Bludau I, Frank M, Dörig C, Cai Y, Heusel M, Rosenberger G, Picotti P, Collins BC, Röst H, Aebersold R. Systematic detection of functional proteoform groups from bottom-up proteomic datasets. Nat Commun. 2021;12(1):3810.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Melani RD, Gerbasi VR, Anderson LC, Sikora JW, Toby TK, Hutton JE, Butcher DS, Negrão F, Seckler HS, Srzentić K, Fornelli L, Camarillo JM, LeDuc RD, Cesnik AJ, Lundberg E, Greer JB, Fellers RT, Robey MT, DeHart CJ, Forte E, Hendrickson CL, Abbatiello SE, Thomas PM, Kokaji AI, Levitsky J, Kelleher NL. The blood proteoform atlas: A reference map of proteoforms in human hematopoietic cells. Science. 2022;375(6579):411–8.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Ardito F, Giuliani M, Perrone D, Troiano G, Lo Muzio L. The crucial role of protein phosphorylation in cell signaling and its use as targeted therapy (Review). Int J Mol Med. 2017;40(2):271–80.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Kaszuba K, Grzybek M, Orłowski A, Danne R, Róg T, Simons K, Coskun Ü, Vattulainen I. N-Glycosylation as determinant of epidermal growth factor receptor conformation in membranes. Proc Natl Acad Sci U S A. 2015;112(14):4334–9.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Chen B, Brown KA, Lin Z, Ge Y. Top-Down proteomics: ready for prime time?? Anal Chem. 2018;90(1):110–27.

Article  PubMed  CAS  Google Scholar 

Liao Y-C, Fulcher JM, Degnan DJ, Williams SM, Bramer LM, Veličković D, Zemaitis KJ, Veličković M, Sontag RL, Moore RJ, Paša-Tolić L, Zhu Y, Zhou M. Spatially resolved Top-Down proteomics of tissue sections based on a microfluidic nanodroplet sample Preparation platform. Mol Cell Proteom 2023, 22 (2).

Toby TK, Fornelli L, Kelleher NL. Progress in Top-Down proteomics and the analysis of proteoforms. Annual Rev Anal Chem. 2016;9(1):499–519.

Article  CAS  Google Scholar 

Prentice BM, Ryan DJ, Van de Plas R, Caprioli RM, Spraggins JM. Enhanced ion transmission efficiency up to m/ Z 24 000 for MALDI protein imaging mass spectrometry. Anal Chem. 2018;90(8):5090–9.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Zemaitis KJ, Veličković D, Kew W, Fort KL, Reinhardt-Szyba M, Pamreddy A, Ding Y, Kaushik D, Sharma K, Makarov AA, Zhou M, Paša-Tolić L. Enhanced Spatial mapping of histone proteoforms in human kidney through MALDI-MSI by High-Field UHMR-Orbitrap detection. Anal Chem. 2022;94(37):12604–13.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Su P, McGee JP, Durbin KR, Hollas MAR, Yang M, Neumann EK, Allen JL, Drown BS, Butun FA, Greer JB, Early BP, Fellers RT, Spraggins JM, Laskin J, Camarillo JM, Kafader JO, Kelleher NL. Highly multiplexed, label-free proteoform imaging of tissues by individual ion mass spectrometry. Sci Adv. 2022;8(32):eabp9929.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Yang M, Unsihuay D, Hu H, Nguele Meke F, Qu Z, Zhang ZY, Laskin J. Nano-DESI mass spectrometry imaging of proteoforms in biological tissues with high Spatial resolution. Anal Chem. 2023;95(12):5214–22.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Hale OJ, Cooper HJ. Native mass spectrometry imaging of proteins and protein complexes by Nano-DESI. Anal Chem. 2021;93(10):4619–27.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Griffiths RL, Konijnenberg A, Viner R, Cooper HJ. Direct mass spectrometry analysis of protein complexes and intact proteins up to > 70 kda from tissue. Anal Chem. 2019;91(11):6962–6.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Hale OJ, Sisley EK, Griffiths RL, Styles IB, Cooper HJ. Native LESA TWIMS-MSI: Spatial, conformational, and mass analysis of proteins and protein complexes. J Am Soc Mass Spectrom. 2020;31(4):873–9.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Hansen J, Sealfon R, Menon R, Eadon MT, Lake BB, Steck B, Anjani K, Parikh S, Sigdel TK, Zhang G, Velickovic D, Barwinska D, Alexandrov T, Dobi D, Rashmi P, Otto EA, Rivera M, Rose MP, Anderton CR, Shapiro JP, Pamreddy A, Winfree S, Xiong Y, He Y, de Boer IH, Hodgin JB, Barisoni L, Naik AS, Sharma K, Sarwal MM, Zhang K, Himmelfarb J, Rovin B, El-Achkar TM, Laszik Z, He JC, Dagher PC, Valerius MT, Jain S, Satlin LM, Troyanskaya OG, Kretzler M, Iyengar R, Azeloglu E. U., A reference tissue atlas for the human kidney. Sci Adv 2022, 8 (23), eabn4965.

Rappez L, Stadler M, Triana S, Gathungu RM, Ovchinnikova K, Phapale P, Heikenwalder M, Alexandrov T. SpaceM reveals metabolic States of single cells. Nat Methods. 2021;18(7):799–805.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Pei S, Michael ARH, Stanislav R, Fatma Ayaloglu B, Joseph BG, Bryan PE, Ryan TF, Michael AC, Jonathan VS, Jared OK, Neil LK. Top-down Proteomics of 10,000 Single Brain Cells. bioRxiv 2023, 2023.05.31.543176.

Pu F, Chiang S, Zhang W, Ouyang Z. Direct sampling mass spectrometry for clinical analysis. Analyst. 2019;144(4):1034–51.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Ryan DJ, Spraggins JM, Caprioli RM. Protein identification strategies in MALDI imaging mass spectrometry: a brief review. Curr Opin Chem Biol. 2019;48:64–72.

Article  PubMed  CAS  Google Scholar 

Han J, Permentier H, Bischoff R, Groothuis G, Casini A, Horvatovich P. Imaging of protein distribution in tissues using mass spectrometry: an interdisciplinary challenge. TRAC Trends Anal Chem. 2019;112:13–28.

Article  CAS  Google Scholar 

Ryan DJ, Patterson NH, Putnam NE, Wilde AD, Weiss A, Perry WJ, Cassat JE, Skaar EP, Caprioli RM, Spraggins JM. MicroLESA: integrating autofluorescence microscopy, in situ Micro-Digestions, and liquid extraction surface analysis for high Spatial resolution targeted proteomic studies. Anal Chem. 2019;91(12):7578–85.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Delcourt V, Franck J, Quanico J, Gimeno J-P, Wisztorski M, Raffo-Romero A, Kobeissy F, Roucou X, Salzet M, Fournier I. Spatially-Resolved Top-down proteomics bridged to MALDI MS imaging reveals the molecular physiome of brain regions. Mol Cell Proteom. 2018;17(2):357–72.

Article  CAS  Google Scholar 

Lubeckyj RA, Sun L. Laser capture microdissection-capillary zone electrophoresis-tandem mass spectrometry (LCM-CZE-MS/MS) for spatially resolved top-down proteomics: a pilot study of zebrafish brain. Mol Omics. 2022;18(2):112–22.

Article  PubMed  PubMed Central  CAS  Google Scholar 

Zhu Y, Piehowski PD, Zhao R, Chen J, Shen Y, Moore RJ, Shukla AK, Petyuk VA, Campbell-Thompson M, Mathews CE, Smith RD, Qian W-J, Kelly RT. Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells. Nat Commun. 2018;9(1):882.

Article  PubMed  PubMed Central  Google Scholar 

Swensen AC, Veličković D, Williams SM, Moore RJ, Day LZ, Niessen S, Hennessy S, Posso C, Monetti M, Qian WJ, Jacobs J, Whiteley L, Zhu Y, Piehowski PD. Proteomic profiling of Intra-Islet features reveals Substructure-Specific protein signatures. Mol Cell Proteom. 2022;21(12):100426.

Article  CAS  Google Scholar 

Gosline SJC, Veličković M, Pino JC, Day LZ, Attah IK, Swensen AC, Danna V, Posso C, Rodland KD, Chen J, Matthews CE, Campbell-Thompson M, Laskin J, Burnum-Johnson K, Zhu Y, Piehowski PD. Proteome mapping of the human pancreatic islet microenvironment reveals Endocrine–Exocrine signaling sphere of influence. Mol Cell Proteom. 2023;22(8):100592.

Article  CAS  Google Scholar 

Zhou M, Uwugiaren N, Williams SM, Moore RJ, Zhao R, Goodlett D, Dapic I, Paša-Tolić L, Zhu Y. Sensitive Top-Down proteomics analysis of a low number of mammalian cells using a nanodroplet sample processing