Pyteomics 4.0: Five Years of Development of a Python Proteomics Framework von Levitsky, Lev I, Klein, Joshua A, Ivanov, Mark V, Gorshkov, Mikhail V

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Boosting MS1-only Proteomics with Machine Learning Allows 2000 Protein Identifications in Single-Shot Human Proteome Analysis Using 5 min HPLC Gradient von Ivanov, Mark V, Bubis, Julia A, Gorshkov, Vladimir, Abdrakhimov, Daniil A, Kjeldsen, Frank, Gorshkov, Mikhail V

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DirectMS1: MS/MS-Free Identification of 1000 Proteins of Cellular Proteomes in 5 Minutes von Ivanov, Mark V, Bubis, Julia A, Gorshkov, Vladimir, Tarasova, Irina A, Levitsky, Lev I, Lobas, Anna A, Solovyeva, Elizaveta M, Pridatchenko, Marina L, Kjeldsen, Frank, Gorshkov, Mikhail V

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Potential of Negative-Ion-Mode Proteomics: An MS1-Only Approach von Penanes, Pelayo A., Gorshkov, Vladimir, Ivanov, Mark V., Gorshkov, Mikhail V., Kjeldsen, Frank

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Predictive chromatography of peptides and proteins as a complementary tool for proteomics von Tarasova, Irina A, Masselon, Christophe D, Gorshkov, Alexander V, Gorshkov, Mikhail V

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Mass Spectrometry-Based Chemical Proteomics for Drug Target Discoveries von Fedorov, Ivan I., Lineva, Victoria I., Tarasova, Irina A., Gorshkov, Mikhail V.

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Biosaur: An open-source Python software for liquid chromatography-mass spectrometry peptide feature detection with ion mobility support von Abdrakhimov, Daniil A., Bubis, Julia A., Gorshkov, Vladimir, Kjeldsen, Frank, Gorshkov, Mikhail V., Ivanov, Mark V.

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Pyteomics—a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics von Goloborodko, Anton A., Levitsky, Lev I., Ivanov, Mark V., Gorshkov, Mikhail V.

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Accelerating photofragmentation UV Spectroscopy–Mass spectrometry fingerprinting for quantification of isomeric peptides von Lobas, Anna A., Solovyeva, Elizaveta M., Saparbaev, Erik, Gorshkov, Mikhail V., Boyarkin, Oleg V.

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High Speed Intact Protein Characterization Using 4X Frequency Multiplication, Ion Trap Harmonization, and 21 Tesla FTICR-MS von Shaw, Jared B, Gorshkov, Mikhail V, Wu, Qinghao, Paša-Tolić, Ljiljana

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AA_stat: Intelligent profiling of in vivo and in vitro modifications from open search results von Levitsky, Lev I., Bubis, Julia A., Gorshkov, Mikhail V., Tarasova, Irina A.

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Towards increasing the performance of FTICR-MS with signal detection at frequency multiples: Signal theory and numerical study von Wu, Qinghao, Gorshkov, Mikhail V., Paša-Tolić, Ljiljana

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Scavager: A Versatile Postsearch Validation Algorithm for Shotgun Proteomics Based on Gradient Boosting von Ivanov, Mark V., Levitsky, Lev I., Bubis, Julia A., Gorshkov, Mikhail V.

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IQMMA: Efficient MS1 Intensity Extraction Pipeline Using Multiple Feature Detection Algorithms for DDA Proteomics von Postoenko, Valeriy I., Garibova, Leyla A., Levitsky, Lev I., Bubis, Julia A., Gorshkov, Mikhail V., Ivanov, Mark V.

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Adenosine‐to‐Inosine RNA Editing in Mouse and Human Brain Proteomes von Levitsky, Lev I., Kliuchnikova, Anna A., Kuznetsova, Ksenia G., Karpov, Dmitry S., Ivanov, Mark V., Pyatnitskiy, Mikhail A., Kalinina, Olga V., Gorshkov, Mikhail V., Moshkovskii, Sergei A.

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Cysteine alkylation methods in shotgun proteomics and their possible effects on methionine residues von Kuznetsova, Ksenia G., Levitsky, Lev I., Pyatnitskiy, Mikhail A., Ilina, Irina Y., Bubis, Julia A., Solovyeva, Elizaveta M., Zgoda, Victor G., Gorshkov, Mikhail V., Moshkovskii, Sergei A.

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Protein corona formed on silver nanoparticles in blood plasma is highly selective and resistant to physicochemical changes of the solution von Gorshkov, Vladimir, Bubis, Julia A, Solovyeva, Elizaveta M, Gorshkov, Mikhail V, Kjeldsen, Frank

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DirectMS1Quant: Ultrafast Quantitative Proteomics with MS/MS-Free Mass Spectrometry von Ivanov, Mark V., Bubis, Julia A., Gorshkov, Vladimir, Tarasova, Irina A., Levitsky, Lev I., Solovyeva, Elizaveta M., Lipatova, Anastasiya V., Kjeldsen, Frank, Gorshkov, Mikhail V.

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Unbiased False Discovery Rate Estimation for Shotgun Proteomics Based on the Target-Decoy Approach von Levitsky, Lev I, Ivanov, Mark V, Lobas, Anna A, Gorshkov, Mikhail V

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On the excessive use of coefficient of variation as a metric of quantitation quality in proteomics von Ivanov, Mark V., Garibova, Leyla A., Postoenko, Valeriy I., Levitsky, Lev I., Gorshkov, Mikhail V.

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