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Data-independent acquisition improves quantitative cross-linking mass spectrometry.

Müller F, Kolbowski L, Bernhardt OM, Reiter L, Rappsilber J.

Mol Cell Proteomics. 2019 Jan 16. pii: mcp.TIR118.001276. doi: 10.1074/mcp.TIR118.001276. [Epub ahead of print]


Accurate Estimation of Context-Dependent False Discovery Rates in Top-Down Proteomics.

LeDuc RD, Fellers RT, Early BP, Greer JB, Shams DP, Thomas P, Kelleher NL.

Mol Cell Proteomics. 2019 Jan 15. pii: mcp.RA118.000993. doi: 10.1074/mcp.RA118.000993. [Epub ahead of print]


Macrophage phosphoproteome analysis reveals MINCLE-dependent and -independent mycobacterial cord factor signaling.

Hansen M, Peltier J, Killy B, Amin B, Bodendorfer B, Härtlova A, Uebel S, Bosmann M, Hofmann J, Büttner C, Ekici AB, Kuttke M, Franzyk H, Foged C, Beer-Hammer S, Schabbauer G, Trost M, Lang R.

Mol Cell Proteomics. 2019 Jan 11. pii: mcp.RA118.000929. doi: 10.1074/mcp.RA118.000929. [Epub ahead of print]


Proteome analysis of human neutrophil granulocytes from patients with monogenic disease using data-independent acquisition.

Grabowski P, Hesse S, Hollizeck S, Rohlfs M, Behrends U, Sherkat R, Tamary H, Ünal E, Somech R, Patıroğlu T, Canzar S, van der Werff Ten Bosch J, Klein C, Rappsilber J.

Mol Cell Proteomics. 2019 Jan 10. pii: mcp.RA118.001141. doi: 10.1074/mcp.RA118.001141. [Epub ahead of print]


High-density peptide arrays help to identify linear immunogenic B cell epitopes in individuals naturally exposed to malaria infection.

Jaenisch T, Heiss K, Fischer N, Geiger C, Bischoff FR, Moldenhauer G, Rychlewski L, Sié A, Coulibaly B, Seeberger PH, Wyrwicz LS, Breitling F, Loeffler FF.

Mol Cell Proteomics. 2019 Jan 10. pii: mcp.RA118.000992. doi: 10.1074/mcp.RA118.000992. [Epub ahead of print]


Phosphoproteomic and functional analyses reveal sperm-specific protein changes downstream of kappa opioid receptor in human spermatozoa.

Urizar-Arenaza I, Osinalde N, Akimov V, Puglia M, Candenas L, Pinto FM, Muñoa-Hoyos I, Gianzo M, Matorras R, Irazusta J, Blagoev B, Subiran N, Kratchmarova I.

Mol Cell Proteomics. 2019 Jan 8. pii: mcp.RA118.001133. doi: 10.1074/mcp.RA118.001133. [Epub ahead of print]


Precision de novo peptide sequencing using mirror proteases of Ac-LysargiNase and trypsin for large-scale proteomics.

Yang H, Li Y, Zhao M, Wu F, Wang X, Xiao W, Wang Y, Zhang J, Wang F, Xu F, Zeng WF, Overall CM, He SM, Chi H, Xu P.

Mol Cell Proteomics. 2019 Jan 8. pii: mcp.TIR118.000918. doi: 10.1074/mcp.TIR118.000918. [Epub ahead of print]


In-depth Proteome of the Hypopharyngeal Glands of Honeybee Workers Reveals Highly Activated Protein and Energy Metabolism in Priming the Secretion of Royal Jelly.

Hu H, Bezabih G, Feng M, Wei Q, Zhang X, Wu F, Meng L, Fang Y, Han B, Ma C, Li J.

Mol Cell Proteomics. 2019 Jan 7. pii: mcp.RA118.001257. doi: 10.1074/mcp.RA118.001257. [Epub ahead of print]


Proteomics reveals multiple phenotypes associated with N-linked glycosylation in Campylobacter jejuni.

Cain JA, Dale AL, Niewold P, Klare WP, Man L, White MY, Scott NE, Cordwell SJ.

Mol Cell Proteomics. 2019 Jan 7. pii: mcp.RA118.001199. doi: 10.1074/mcp.RA118.001199. [Epub ahead of print]


Celastrol protects from cholestatic liver injury though modulation of SIRT1-FXR signaling.

Zhao Q, Liu F, Cheng Y, Xiao XR, Hu DD, Tang YM, Bao WM, Yang JH, Jiang T, Hu JP, Gonzalez F, Li F.

Mol Cell Proteomics. 2019 Jan 7. pii: mcp.RA118.000817. doi: 10.1074/mcp.RA118.000817. [Epub ahead of print]


Decreased antibiotic susceptibility driven by global remodeling of the Klebsiella pneumoniae proteome.

Keasey SL, Suh MJ, Das S, Blancett CD, Zeng X, Andresson T, Sun MG, Ulrich RG.

Mol Cell Proteomics. 2019 Jan 7. pii: mcp.RA118.000739. doi: 10.1074/mcp.RA118.000739. [Epub ahead of print]


Quantitative mass spectrometry to interrogate proteomic heterogeneity in metastatic lung adenocarcinoma and validate a novel somatic mutation CDK12-G879V.

Zhang X, Nguyen KD, Rudnick P, Roper N, Kawaler E, Maity TK, Awasthi S, Gao S, Biswas R, Venugopalan A, Cultraro CM, Fenyö D, Guha U.

Mol Cell Proteomics. 2019 Jan 7. pii: mcp.RA118.001266. doi: 10.1074/mcp.RA118.001266. [Epub ahead of print]


Changes in synaptic proteins precede neurodegeneration markers in preclinical Alzheimer's disease cerebrospinal fluid.

Lleó A, Núñez-Llaves R, Alcolea D, Chiva C, Balateu-Paños D, Colom-Cadena M, Gomez-Giro G, Muñoz L, Querol-Vilaseca M, Pegueroles J, Rami L, Lladó A, Molinuevo J, Tainta M, Clarimón J, Spires-Jones T, Blesa R, Fortea J, Martínez-Lage P, Sánchez-Valle R, Sabidó E, Bayés À, Belbin O.

Mol Cell Proteomics. 2019 Jan 3. pii: mcp.RA118.001290. doi: 10.1074/mcp.RA118.001290. [Epub ahead of print]


Initial Guidelines for Manuscripts Employing Data-independent Acquisition Mass Spectrometry for Proteomic Analysis.

Chalkley RJ, MacCoss MJ, Jaffe JD, Röst HL.

Mol Cell Proteomics. 2019 Jan;18(1):1-2. doi: 10.1074/mcp.E118.001286. No abstract available.


Protein-Level Interactions as Mediators of Sexual Conflict in Ants.

Dosselli R, Grassl J, den Boer SPA, Kratz M, Moran JM, Boomsma JJ, Baer B.

Mol Cell Proteomics. 2018 Dec 31. pii: mcp.RA118.000941. doi: 10.1074/mcp.RA118.000941. [Epub ahead of print]


Simultaneous Quantification of Protein Expression and Modifications by Top-down Targeted Proteomics: A Case of Sarcomeric Subproteome.

Lin Z, Wei L, Cai W, Zhu Y, Tucholski T, Mitchell SD, Guo W, Ford SP, Diffee GM, Ge Y.

Mol Cell Proteomics. 2018 Dec 27. pii: mcp.TIR118.001086. doi: 10.1074/mcp.TIR118.001086. [Epub ahead of print]


Identification of Novel Protein Targets of Dimethyl Fumarate Modification in Neurons and Astrocytes Reveals Actions Independent of Nrf2 Stabilization.

Piroli GG, Manuel AM, Patel T, Walla MD, Shi L, Lanci SA, Wang J, Galloway A, Ortinski PI, Smith DS, Frizzell N.

Mol Cell Proteomics. 2018 Dec 26. pii: mcp.RA118.000922. doi: 10.1074/mcp.RA118.000922. [Epub ahead of print]


HLA-DO modulates the diversity of the MHC-II self-peptidome.

Nanaware PP, Jurewicz MM, Leszyk J, Shaffer SA, Stern LJ.

Mol Cell Proteomics. 2018 Dec 20. pii: mcp.RA118.000956. doi: 10.1074/mcp.RA118.000956. [Epub ahead of print]


psims - A declarative writer for mzML and mzIdentML for Python.

Klein JA, Zaia J.

Mol Cell Proteomics. 2018 Dec 18. pii: mcp.RP118.001070. doi: 10.1074/mcp.RP118.001070. [Epub ahead of print]


A curated resource for phosphosite-specific signature analysis.

Krug K, Mertins P, Zhang B, Hornbeck P, Raju R, Ahmad R, Szucs M, Mundt F, Forestier D, Jane-Valbuena J, Keshishian H, Gillette MA, Tamayo P, Mesirov JP, Jaffe JD, Carr SA, Mani DR.

Mol Cell Proteomics. 2018 Dec 18. pii: mcp.TIR118.000943. doi: 10.1074/mcp.TIR118.000943. [Epub ahead of print]

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