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1.

Method for Identification of Threonine Isoforms in Peptides by Ultraviolet Photofragmentation of Cold Ions.

Solovyeva EM, Kopysov VN, Pereverzev AY, Lobas AA, Moshkovskii SA, Gorshkov MV, Boyarkin OV.

Anal Chem. 2019 May 21;91(10):6709-6715. doi: 10.1021/acs.analchem.9b00770. Epub 2019 May 10.

PMID:
31042365
2.

Pyteomics 4.0: Five Years of Development of a Python Proteomics Framework.

Levitsky LI, Klein JA, Ivanov MV, Gorshkov MV.

J Proteome Res. 2019 Feb 1;18(2):709-714. doi: 10.1021/acs.jproteome.8b00717. Epub 2019 Jan 8.

PMID:
30576148
3.

Scavager: A Versatile Postsearch Validation Algorithm for Shotgun Proteomics Based on Gradient Boosting.

Ivanov MV, Levitsky LI, Bubis JA, Gorshkov MV.

Proteomics. 2019 Feb;19(3):e1800280. doi: 10.1002/pmic.201800280. Epub 2018 Dec 27.

PMID:
30537264
4.

Validation of Peptide Identification Results in Proteomics Using Amino Acid Counting.

Bubis JA, Levitsky LI, Ivanov MV, Gorshkov MV.

Proteomics. 2018 Dec;18(23):e1800117. doi: 10.1002/pmic.201800117. Epub 2018 Nov 2.

PMID:
30307114
5.

Proteogenomics of Adenosine-to-Inosine RNA Editing in the Fruit Fly.

Kuznetsova KG, Kliuchnikova AA, Ilina IU, Chernobrovkin AL, Novikova SE, Farafonova TE, Karpov DS, Ivanov MV, Goncharov AO, Ilgisonis EV, Voronko OE, Nasaev SS, Zgoda VG, Zubarev RA, Gorshkov MV, Moshkovskii SA.

J Proteome Res. 2018 Nov 2;17(11):3889-3903. doi: 10.1021/acs.jproteome.8b00553. Epub 2018 Oct 17.

PMID:
30298734
6.

Multiplexed Middle-Down Mass Spectrometry as a Method for Revealing Light and Heavy Chain Connectivity in a Monoclonal Antibody.

Srzentić K, Nagornov KO, Fornelli L, Lobas AA, Ayoub D, Kozhinov AN, Gasilova N, Menin L, Beck A, Gorshkov MV, Aizikov K, Tsybin YO.

Anal Chem. 2018 Nov 6;90(21):12527-12535. doi: 10.1021/acs.analchem.8b02398. Epub 2018 Oct 12.

PMID:
30252447
7.

Profiling modifications for glioblastoma proteome using ultra-tolerant database search: Are the peptide mass shifts biologically relevant or chemically induced?

Tarasova IA, Chumakov PM, Moshkovskii SA, Gorshkov MV.

J Proteomics. 2019 Jan 16;191:16-21. doi: 10.1016/j.jprot.2018.05.010. Epub 2018 May 17.

PMID:
29777870
8.

Chemical-Mediated Digestion: An Alternative Realm for Middle-down Proteomics?

Srzentić K, Zhurov KO, Lobas AA, Nikitin G, Fornelli L, Gorshkov MV, Tsybin YO.

J Proteome Res. 2018 Jun 1;17(6):2005-2016. doi: 10.1021/acs.jproteome.7b00834. Epub 2018 May 18.

PMID:
29722266
9.

IdentiPy: An Extensible Search Engine for Protein Identification in Shotgun Proteomics.

Levitsky LI, Ivanov MV, Lobas AA, Bubis JA, Tarasova IA, Solovyeva EM, Pridatchenko ML, Gorshkov MV.

J Proteome Res. 2018 Jul 6;17(7):2249-2255. doi: 10.1021/acs.jproteome.7b00640. Epub 2018 Jun 18.

PMID:
29682971
10.

FractionOptimizer: a method for optimal peptide fractionation in bottom-up proteomics.

Solovyeva EM, Lobas AA, Kopylov AT, Ilina IY, Levitsky LI, Moshkovskii SA, Gorshkov MV.

Anal Bioanal Chem. 2018 Jun;410(16):3827-3833. doi: 10.1007/s00216-018-1054-2. Epub 2018 Apr 17.

PMID:
29663059
11.

Proteogenomics of Malignant Melanoma Cell Lines: The Effect of Stringency of Exome Data Filtering on Variant Peptide Identification in Shotgun Proteomics.

Lobas AA, Pyatnitskiy MA, Chernobrovkin AL, Ilina IY, Karpov DS, Solovyeva EM, Kuznetsova KG, Ivanov MV, Lyssuk EY, Kliuchnikova AA, Voronko OE, Larin SS, Zubarev RA, Gorshkov MV, Moshkovskii SA.

J Proteome Res. 2018 May 4;17(5):1801-1811. doi: 10.1021/acs.jproteome.7b00841. Epub 2018 Apr 16.

PMID:
29619825
12.

High Speed Intact Protein Characterization Using 4X Frequency Multiplication, Ion Trap Harmonization, and 21 Tesla FTICR-MS.

Shaw JB, Gorshkov MV, Wu Q, Paša-Tolić L.

Anal Chem. 2018 May 1;90(9):5557-5562. doi: 10.1021/acs.analchem.7b04606. Epub 2018 Apr 13.

PMID:
29613776
13.

Comparative proteomics as a tool for identifying specific alterations within interferon response pathways in human glioblastoma multiforme cells.

Tarasova IA, Tereshkova AV, Lobas AA, Solovyeva EM, Sidorenko AS, Gorshkov V, Kjeldsen F, Bubis JA, Ivanov MV, Ilina IY, Moshkovskii SA, Chumakov PM, Gorshkov MV.

Oncotarget. 2017 Nov 29;9(2):1785-1802. doi: 10.18632/oncotarget.22751. eCollection 2018 Jan 5.

14.

Identification of isoforms of aspartic acid residues in peptides by 2D UV-MS fingerprinting of cold ions.

Kopysov V, Gorshkov MV, Boyarkin OV.

Analyst. 2018 Feb 12;143(4):833-836. doi: 10.1039/c7an02044a.

PMID:
29379909
15.

Brute-Force Approach for Mass Spectrometry-Based Variant Peptide Identification in Proteogenomics without Personalized Genomic Data.

Ivanov MV, Lobas AA, Levitsky LI, Moshkovskii SA, Gorshkov MV.

J Am Soc Mass Spectrom. 2018 Feb;29(2):435-438. doi: 10.1007/s13361-017-1859-9. Epub 2018 Jan 3.

PMID:
29299837
16.

MS/MS-Free Protein Identification in Complex Mixtures Using Multiple Enzymes with Complementary Specificity.

Ivanov MV, Tarasova IA, Levitsky LI, Solovyeva EM, Pridatchenko ML, Lobas AA, Bubis JA, Gorshkov MV.

J Proteome Res. 2017 Nov 3;16(11):3989-3999. doi: 10.1021/acs.jproteome.7b00365. Epub 2017 Sep 28.

PMID:
28905631
17.

Influence of the Number of Axial Bexarotene Ligands on the Cytotoxicity of Pt(IV) Analogs of Oxaliplatin.

Nosova YN, Zenin IV, Maximova VP, Zhidkova EM, Kirsanov KI, Lesovaya EA, Lobas AA, Gorshkov MV, Kovaleva ON, Milaeva ER, Galanski M, Keppler BK, Nazarov AA.

Bioinorg Chem Appl. 2017;2017:4736321. doi: 10.1155/2017/4736321. Epub 2017 Jul 19.

18.

Correction: Predictive chromatography of peptides and proteins as a complementary tool for proteomics.

Tarasova IA, Masselon CD, Gorshkov AV, Gorshkov MV.

Analyst. 2017 May 30;142(11):2054. doi: 10.1039/c7an90034a.

PMID:
28530288
19.

Comparison of False Discovery Rate Control Strategies for Variant Peptide Identifications in Shotgun Proteogenomics.

Ivanov MV, Lobas AA, Karpov DS, Moshkovskii SA, Gorshkov MV.

J Proteome Res. 2017 May 5;16(5):1936-1943. doi: 10.1021/acs.jproteome.6b01014. Epub 2017 Mar 31.

PMID:
28317375
20.

Comparative evaluation of label-free quantification methods for shotgun proteomics.

Bubis JA, Levitsky LI, Ivanov MV, Tarasova IA, Gorshkov MV.

Rapid Commun Mass Spectrom. 2017 Apr 15;31(7):606-612. doi: 10.1002/rcm.7829.

PMID:
28097710

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