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Peaks version 7

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PEAKS (version 7.0) is a software tool for protein identification and characterization. It is designed to analyze mass spectrometry data and provide insights into protein sequences and post-translational modifications.

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Lab products found in correlation

Masshunter software, by Agilent Technologies (1 mentions) Q exactive, by Thermo Fisher Scientific (1 mentions) Ultimate 3000 uplc, by Thermo Fisher Scientific (1 mentions)

4 protocols using peaks version 7

1

Synechocystis PSII Protein Identification

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The raw LC-MS/MS files were searched for Synechocystis PSII proteins using PEAKS (version 7.0, Bioinformatics Solutions Inc.), with the built-in decoy fusion database used for false discovery rate calculation (65 ). The oxidative modifications listed in table S1 were included in the search, as well as carbamidomethylation (C, D, H, K, and E, peptide N terminus), +57.0215 Da; deamidation (N and Q), +0.9840 Da; acetylation of protein N terminus, +42.0106 Da; and carbamylation (K, peptide N terminus), +43.0058 Da. Additional search parameters are as follows: precursor-ion mass tolerance, 10.0 parts per million (ppm); fragment-ion mass tolerance, 0.02 Da; maximum three variable modifications per peptide; maximum three missed cleavages; maximum one nonspecific cleavage. Peptides were identified with a 0.1% false discovery rate (−10 log P ≥ 40). For every candidate oxidized residue that met the 0.1% false discovery threshold, product-ion (MS/MS) spectra were inspected manually to confirm data quality, and spectra were rejected if the oxidation could not be localized to a single residue, if the precursor-ion mass error was greater than 5.0 ppm, or if the peptide was a product of a nonspecific cleavage. MS data are available through Chorus (http://chorusproject.org), project #1388. Protein visualization was performed using VMD (66 ).
Weisz D.A., Gross M.L, & Pakrasi H.B. (2017). Reactive oxygen species leave a damage trail that reveals water channels in Photosystem II. Science Advances, 3(11), eaao3013.
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2

Oxidation and Reduction Analysis of C3S msrA

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85 μM C3S msrA was treated with 1 mM hydrogen peroxide for 15 min at 37°C. The solution was then incubated with 10 mM DTT for 10 min to stop the reaction and reduce any sulfenylamide present. It was then dialyzed against 50 mM Tris/1 mM DTPA, pH 7.4 at 4°C. Twenty μg protein in 21 μl was digested at 37°C overnight with 1 μg chymotrypsin (# 84975820, Boeringer Mannheim). The digestion was stopped by adding 0.2 μl of 50% acetic acid, giving a final concentration of 0.5%. 7.5 μg was analyzed by reverse phase HPLC- tandem mass spectrometry as described above for protein mass spectroscopy except that the acetonitrile gradient was developed at 1%/min from 0 to 45%. Spectra were deconvoluted with the same Agilent MassHunter software and MS/MS spectra were matched to those predicted with GPMAW and confirmed by de novo sequencing with PEAKS version 7.0 (Bioinformatics Solutions, Ontario, Canada).
Kim G, & Levine R.L. (2016). A Methionine Residue Promotes Hyperoxidation of the Catalytic Cysteine of Mouse Methionine Sulfoxide Reductase A. Biochemistry, 55(25), 3586-3593.
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3

Mass Spectrometry Analysis of USP4 Ubiquitylation

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Samples were analyzed using nano liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS) in HCD mode as described previously (Fischer and Kessler, 2015 (link)). Raw MS data were processed and analyzed by PEAKS Version 7 (Bioinformatics Solutions) using HCD fragmentation spectra. MS/MS spectra were searched against the Swissprot (21,039 human sequence entries) database allowing for variable post-translational modifications to be applied to the de novo identified peptides. See Table S4 for identified ubiquitylations on USP4 WT and CD upon immunoprecipitation with a GFP antibody from 293FT lysates. Amino acids in bold indicate previously described USP4 ubiquitylations.
Wijnhoven P., Konietzny R., Blackford A.N., Travers J., Kessler B.M., Nishi R, & Jackson S.P. (2015). USP4 Auto-Deubiquitylation Promotes Homologous Recombination. Molecular Cell, 60(3), 362-373.
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4

Proteomic Profiling via LC-MS/MS

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Samples were analysed using a nano-liquid chromatography tandem mass spectrometry (LC-MS/MS) system consisting of a Dionex Ultimate 3000 UPLC coupled to a hybrid quadrupole orbitrap instrument (Q Exactive, Thermo). Samples were loaded at a flow rate of 20 µL/min onto a PepMAP pre-column (C18, 300 µm×5mm, 5 µm particle size, Thermo) for one minute and separated at a flow rate of 250 nl/min on an nEASY column (C18, 75 µm×500 mm, 2 µm particle size, Thermo) for 60 minutes using a gradient of 2%–35% acetonitrile (v/v) in 5% DMSO (v/v) and 0.1% formic acid (v/v). All scans were performed at a resolution of 70,000 at 200 mass/charge and the 15 most abundant precursors were selected for HCD fragmentation. Raw MS data were de novo sequenced by PEAKS Version 7 (Bioinformatics Solutions) with search criteria at 10 ppm for MS1 and 0.05 Da for MS2. A database search (human SwissProt, 85,809 sequences) with subsequent posttranslational modification searches, where all modifications reported in UNIMOD were considered, was then applied to the de novo identified MS/MS spectra. False discovery rates of 1% threshold were applied. MS/MS spectra with phosphorylation modifications were inspected manually.
Mathea S., Abdul Azeez K.R., Salah E., Tallant C., Wolfreys F., Konietzny R., Fischer R., Lou H.J., Brennan P.E., Schnapp G., Pautsch A., Kessler B.M., Turk B.E, & Knapp S. (2016). Structure of the Human Protein Kinase ZAK in Complex with Vemurafenib. ACS chemical biology, 11(6), 1595-1602.
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