Pepmix 2

Manufactured by Bruker

Sourced in Germany

The PepMix II is a laboratory equipment product designed for the synthesis of peptides. It provides a controlled environment and tools for the chemical synthesis and purification of peptide molecules. The core function of the PepMix II is to facilitate the step-by-step assembly of peptides from amino acid building blocks.

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Lab products found in correlation

Profiling kit 1000 c8 mb, by Bruker (2 mentions) Protmix 1, by Bruker (2 mentions) 2 5 dihydroxybenzoic acid, by Merck Group (1 mentions) Data analysis software, by Bruker (1 mentions) Ultraflex 3 maldi tof instrument, by Bruker (1 mentions) Solarix ft icr mass spectrometer, by Bruker (1 mentions) Mascot search engine, by Matrix Science (1 mentions) Smartbeam 2 uv laser, by Bruker (1 mentions)

7 protocols using pepmix 2

Analytical Characterization of Materials

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2,5-Dihydroxybenzoic acid (DHB, > 99%)
and
HPLC-grade methanol, ethanol, hexane, and chloroform were obtained
from Sigma-Aldrich (Sigma-Aldrich, Zwijndrecht, NL). Blue and green
acrylic paints were purchased from a local arts supplier (Maastricht,
NL). Indium-Tin-Oxide (ITO) coated glass slides from Delta Technologies
(Loveland, U.S.A.) were cleaned with lab-grade hexane and ethanol.
Transmission electron microscopy (TEM) grids with hexagonal meshes
of size 300 were obtained from Agar Scientific, Ltd. (Stansted, Essex,
U.K.). Peptide calibration mixture II, “Pepmix II” was
purchased from Bruker Daltonik, GMBH (Bremen, DE). Remaining mouse
brain tissue samples from a different study were used.^{20 (link)}

Krijnen K., Keelor J.D., Böhm S., Ellis S.R., Köster C., Höhndorf J., Heeren R.M, & Anthony I.G. (2023). A Multimodal SIMS/MALDI Mass Spectrometry Imaging Source with Secondary Electron Imaging Capabilities for Use with timsTOF Instruments. Journal of the American Society for Mass Spectrometry, 34(4), 720-727.

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MALDI-FTICR MS Analysis of Siderophores

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Two microliters of the prepared solutions were spotted on a ground steel MALDI plate, dried and covered by 1 μl of α-cyano-4-hydroxycinnamic acid (CHCA; 10 mg/ml in 50% ACN/0.1% trifluoroacetic acid) matrix. MALDI MS analyses were performed using the Solarix FT-ICR 12T (Bruker Daltonics, USA) mass spectrometer. All measurements were acquired in positive ion mode in a 150–1500 m/z mass range after an external calibration against Pepmix II (Bruker Daltonics) and clusters of CHCA with a mass accuracy better than 2 ppm. To increase ion intensity, the continuous accumulation of selected ions (CASI) mode with a quadrupole-narrowing window in the 500–1000 mass range was used. Desorption/ionization of siderophores was performed using SmartBeam II laser (laser power of 40%, 200 shots, 2 kHz), and instrument parameters was tuned to optimal absolute ion signal intensity. Mass spectra of selected ions were collected at a 1 Da isolation width and 20–25 V collision energy. Final spectra represented an average of 16 or 32 acquired scans. Data were processed using the DataAnalysis software (v.4.1, Bruker Daltonics) and siderophores were annotated in CycloBranch (v.2.0.8) against our databases (Pluháček et al., 2016 (link); Novák et al., 2020 (link)).

Le Govic Y., Havlíček V., Capilla J., Luptáková D., Dumas D., Papon N., Le Gal S., Bouchara J.P, & Vandeputte P. (2020). Synthesis of the Hydroxamate Siderophore Nα-Methylcoprogen B in Scedosporium apiospermum Is Mediated by sidD Ortholog and Is Required for Virulence. Frontiers in Cellular and Infection Microbiology, 10, 587909.

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MALDI-TOF Protein Profiling Protocol

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Profiling Kit 1000 C8-MB, α-cyano-4-hydroxycinnamic acid (CHCA), Protein Calibration Standard I (ProtMix I) and Peptide Calibration Standard II (PepMix II) were provided by Bruker Daltonics GmbH (Bremen, Germany).

Chinello C., Cazzaniga M., De Sio G., Smith A.J., Grasso A., Rocco B., Signorini S., Grasso M., Bosari S., Zoppis I., Mauri G, & Magni F. (2015). Tumor size, stage and grade alterations of urinary peptidome in RCC. Journal of Translational Medicine, 13, 332.

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MALDI-TOF Mass Spectrometry of Hemoglobin

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Peptide mass mapping spectra were acquired on an Ultraflex III MALDI-TOF instrument in the mass range of 700–4000 Da and calibrated externally using a peptide standard PepMix II (Bruker Daltonics). At least two peptides per sample were selected for MS/MS sequencing using LIFT technology. MS/MS data were searched against the SwissProt20171124 database subset of vertebrate proteins using in-house MASCOT search engine (Matrix Science) with the following search settings; enzyme: trypsin, variable modification: oxidation (M), MS mass tolerance: 20 ppm, MS/MS mass tolerance: 0.6 Da, number of missed cleavages: 1. MS/MS spectra with a MOWSE score over the threshold of 25 (calculated for the settings used) were considered as reliably identified. Peptide sequences of Neumann’s grass rat hemoglobin were derived by de novo MS/MS sequencing. One MALDI peptide mass map (sample EME8) was also measured on a Solarix FT-ICR mass spectrometer (Bruker Daltonics) with mass accuracy below 1 ppm.

Hlavackova K., Dvorak V., Chaskopoulou A., Volf P, & Halada P. (2019). A novel MALDI-TOF MS-based method for blood meal identification in insect vectors: A proof of concept study on phlebotomine sand flies. PLoS Neglected Tropical Diseases, 13(9), e0007669.

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Profiling Kit 1000 C8-MB Protocol

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Profiling Kit 1000 C8-MB, α-cyano-4-hydroxycinnamic acid (CHCA), Protein Calibration Standard I (ProtMix I) and Peptide Calibration Standard II (PepMix II) were supplied by Bruker Daltonics GmbH (Bremen, Germany).

Chinello C., Cazzaniga M., De Sio G., Smith A.J., Gianazza E., Grasso A., Rocco F., Signorini S., Grasso M., Bosari S., Zoppis I., Dakna M., van der Burgt Y.E., Mauri G, & Magni F. (2014). Urinary Signatures of Renal Cell Carcinoma Investigated by Peptidomic Approaches. PLoS ONE, 9(9), e106684.

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Rat Brain Imaging by MALDI-FT-ICR MS

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Experimental details about animals, tissue sectioning, and matrix application can be found in the Supporting Information. The rat sagittal brain slice was prepared and imaged to generate 39 775 pixels. MSI was performed on a solariX 7T MALDI FT-ICR mass spectrometer (Bruker Corp., Billerica, MA) equipped with an atmospheric pressure ionization dual ESI/MALDI source operating at ~2.65 mbar. A mass window of m/z 150–1200 was selected, yielding transients with 0.734 s duration, which resulted in a resolving power of 93 000 at m/z 700. MALDI mass spectra were acquired in positive-mode using a smartbeam-II UV laser (Bruker Corp.) in ‘minimum’ mode with a 50-μm raster width. Each MALDI acquisition consisted of 400 laser shots at a frequency of 1000 Hz. External calibration was performed using PepMix II (Bruker Corp.). The total time for data acquisition was 8 h and the entire imaging experiment took 15 h, with an ~0.85 s measurement overhead per pixel (e.g., time spent on multiple laser shots, ion accumulation, stage movement, and some online processing). The acquired dataset was used as the gold standard to evaluate the subspace approach. We would like to note that these measurement overheads are instrument- and experiment-dependent, and can be further reduced by optimizing various experimental parameters, but are not the focus of this paper.

Xie Y.R., Castro D.C., Lam F, & Sweedler J.V. (2020). Accelerating Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry Imaging Using a Subspace Approach. Journal of the American Society for Mass Spectrometry, 31(11), 2338-2347.

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Single Cell Mass Spectrometry of Aplysia Neurons

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Single cell mass spectra were acquired using an ultrafleXtreme II MALDI-TOF/TOF mass spectrometer (Bruker Corp) using positive reflectron mode and an m/z window of 480 to 5500, externally calibrated using Bruker Pep Mix II and bovine insulin. Each mass spectrum was acquired using 1000 laser shots at 1000 Hz and a 100-μm-diameter footprint using the “ultra” laser setting. microMS-generated xeo geometry files were used to automate data acquisition in each ROI. Since many of the targeted Aplysia neurons were larger than the 100-μm laser footprint, and MALDI matrix crystallization did not always occur atop these larger cells, four mass spectra were acquired at different points centered on the edge of each cell. To reduce experimental errors, the slides, ROIs, and cells within each ROI were sampled in a random order.

Chan-Andersen P.C., Romanova E.V., Rubakhin S.S, & Sweedler J.V. (2022). Profiling 26,000 Aplysia californica neurons by single cell mass spectrometry reveals neuronal populations with distinct neuropeptide profiles. The Journal of Biological Chemistry, 298(8), 102254.

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