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Pepmap trap

Manufactured by Thermo Fisher Scientific
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The PepMap trap is a laboratory instrument designed for sample preparation in proteomics analysis. It functions as a pre-concentration and desalting device for liquid chromatography-mass spectrometry (LC-MS) workflows. The PepMap trap allows for the efficient capture, concentration, and purification of peptides prior to separation and detection.

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Lab products found in correlation

Ultimate 3000 nuplc, by Thermo Fisher Scientific (6 mentions) Fusion lumos mass spectrometer, by Thermo Fisher Scientific (3 mentions) Fusion lumos, by Thermo Fisher Scientific (1 mentions) Ultimate 3000 rslc, by Thermo Fisher Scientific (1 mentions) Scaffold dia v 2, by Proteome Software (1 mentions)

Close spelling variants of this product

Acclaim PepMap 100 C18 trap Acclaim PepMap 100 C18 trap column Acclaim PepMap 100 C18 5 mm ×300 μm trap column PepMap 100 C18 trap column Acclaim PepMap 100 trap column C18 PepMap trap column PepMap cartridge trap Acclaim PepMap trap cartridge RP C18 EASY-Spray Pepmap C18 trap column Acclaim PepMap trap column

8 protocols using pepmap trap

1

High-Resolution Peptide Separation and DIA Analysis

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Peptides were desalted and trapped on a Thermo PepMap trap and separated on an Easy-spray 100 μm × 25 cm C18 column using a Dionex Ultimate 3,000 nUPLC at 200 nL/min. Solvent A = 0.1% formic acid, Solvent B = 100% Acetonitrile 0.1% formic acid. Gradient conditions = 2% B to 50% B over 60 min, followed by a 50%–99% B in 6 min and then held for 3 min than 99% B to 2%B in 2 min and total run time of 90 min using Thermo Scientific Fusion Lumos mass spectrometer. The samples were run in DIA mode; mass spectra were acquired using a collision energy of 35, resolution of 30 K, maximum inject time of 54 ms and a AGC target of 50K, using staggered isolation windows of 12 Da in the m/z range 400–1,000 m/z.
Saha B., Salemi M., Williams G.L., Oh S., Paffett M.L., Phinney B, & Mandell M.A. (2022). Interactomic analysis reveals a homeostatic role for the HIV restriction factor TRIM5α in mitophagy. Cell reports, 39(6), 110797.
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2

High-Resolution Peptide Separation and DIA Analysis

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Peptides were desalted and trapped on a Thermo PepMap trap and separated on an Easy-spray 100 μm × 25 cm C18 column using a Dionex Ultimate 3,000 nUPLC at 200 nL/min. Solvent A = 0.1% formic acid, Solvent B = 100% Acetonitrile 0.1% formic acid. Gradient conditions = 2% B to 50% B over 60 min, followed by a 50%–99% B in 6 min and then held for 3 min than 99% B to 2%B in 2 min and total run time of 90 min using Thermo Scientific Fusion Lumos mass spectrometer. The samples were run in DIA mode; mass spectra were acquired using a collision energy of 35, resolution of 30 K, maximum inject time of 54 ms and a AGC target of 50K, using staggered isolation windows of 12 Da in the m/z range 400–1,000 m/z.
Saha B., Salemi M., Williams G.L., Oh S., Paffett M.L., Phinney B, & Mandell M.A. (2022). Interactomic analysis reveals a homeostatic role for the HIV restriction factor TRIM5α in mitophagy. Cell reports, 39(6), 110797.
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3

DIA-Based Proteomics Workflow

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The next steps were processed at the UC Davis Proteomics Core Facility. Peptides were trapped on a Thermo PepMap trap and separated on an Easy-spray 100 um x 25 cm C18 column using a Dionex Ultimate 3000 nUPLC at 200 nl/min. Solvent A= 0.1% formic acid, Solvent B = 100% Acetonitrile 0.1% formic acid. Gradient conditions = 2%B to 50%B over 60 minutes, followed by a 50%−99% B in 6 minutes and then held for 3 minutes than 99%B to 2%B in 2 minutes and total run time of 90 minutes using Thermo Scientific Fusion Lumos mass spectrometer running in Data Independent Acquisition (DIA) mode. Each individual sample was run using a 2x gas phase fractionation strategy where each sample was analyzed two times with the first gas phase fraction being between 360–760 m/z, the second being 760–1158 m/z. Both gas phase fractions used 4 Da non-overlapping windows.
Kilinc S., Paisner R., Camarda R., Gupta S., Momcilovic O., Kohnz R.A., Avsaroglu B., L’Etoile N.D., Perera R.M., Nomura D.K, & Goga A. (2021). Oncogene Regulated Release of Extracellular Vesicles. Developmental cell, 56(13), 1989-2006.e6.
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4

Proteomics Analysis by DIA-MS

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All proteomics methods were performed at the UC Davis Proteomics Core Facility. Peptides were trapped on a Thermo PepMap trap and separated on an Easy-spray 100 μm × 25 cm C18 column using a Dionex Ultimate 3000 nUPLC at 200 nL/min. Solvent A = 0.1% formic acid and Solvent B = 100% acetonitrile with 0.1% formic acid. Gradient conditions were 2% B to 50% B over 60 min, followed by 50% to 99% B in six min held for three min, then 99% B to 2% B in two min for a total run time of 90 min using a Thermo Scientific Fusion Lumos mass spectrometer running in data independent acquisition (DIA) mode.
Helena Duarte Sagawa C., Zaini P.A., de A. B. Assis R., Saxe H., Salemi M., Jacobson A., Wilmarth P.A., Phinney B.S, & M. Dandekar A. (2020). Deep Learning Neural Network Prediction Method Improves Proteome Profiling of Vascular Sap of Grapevines during Pierce’s Disease Development. Biology, 9(9), 261.
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5

Peptide Separation and Analysis by nLC-MS/MS

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Peptides were desalted and trapped on a Thermo PepMap trap and separated on an Easy-spray 100 μm × 25 cm C18 column using a Dionex Ultimate 3,000 nUPLC at 200 nL/min. Solvent A = 0.1% formic acid, Solvent B = 100% Acetonitrile 0.1% formic acid. Gradient conditions = 2% B to 50% B over 60 min, followed by a 50%–99% B in 6 min and then held for 3 min than 99% B to 2% B in 2 min and total run time of 90 min using Thermo Scientific Fusion Lumos mass spectrometer. The samples were run in DIA mode; mass spectra were acquired using a collision energy of 35, resolution of 30 K, maximum inject time of 54 ms and an AGC target of 50K, using staggered isolation windows of 12 Da in the m/z range 400–1,000 m/z.
Wang F., Peters R., Jia J., Mudd M., Salemi M., Allers L., Javed R., Duque T.L., Paddar M.A., Trosdal E.S., Phinney B, & Deretic V. (2023). ATG5 provides host protection acting as a switch in the atg8ylation cascade between autophagy and secretion. Developmental cell, 58(10), 866-884.e8.
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6

Comprehensive Proteomic Analysis of Thirdhand Smoke

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Peptides were desalted and trapped on a Thermo PepMap trap and separated on an Easy-spray 100 μm x 25 cm C18 column using a Dionex Ultimate 3000 RSLC at 200 nL/min. Solvent A = 0.1% formic acid, and solvent B = 100% acetonitrile 0.1% formic acid. Gradient conditions = 2% B to 50% B over 60 min, followed by a 50%–99% B in 6 min, then held for 3 min, then 99% B to 2% B in 2 min with a total run time of 90 min using a Thermo Scientific Fusion Lumos mass spectrometer. Two data acquisition modes were employed: data-dependent analysis DDA and data-independent analysis, DIA. The DDA mode was used to build spectral libraries, which were used to perform deep searches on the samples, run in DIA mode. To obtain the DDA runs, we pooled peptides from all our thirdhand smoke samples. Then, this pooled sample was divided, and eight DDA injections were performed. MS data for samples run in DIA mode cover the entire range of m/z 400–1200. Both DDA and DIA data were acquired using a collision energy of 35, resolution of 30 K, maximum inject time of 54 ms and a AGC target of 50 K, using staggered isolation windows of 12 Da.
Sakamaki-Ching S., Schick S., Grigorean G., Li J, & Talbot P. (2022). Dermal thirdhand smoke exposure induces oxidative damage, initiates skin inflammatory markers, and adversely alters the human plasma proteome. eBioMedicine, 84, 104256.
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7

Proteome Analysis by Dionex DIA-MS

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The next steps were processed at the UC Davis Proteomics Core Facility. Peptides were trapped on a Thermo PepMap trap and separated on an Easy-spray 100 um x 25 cm C18 column using a Dionex Ultimate 3000 nUPLC at 200 nl/min. Solvent A= 0.1% formic acid, Solvent B = 100% Acetonitrile 0.1% formic acid. Gradient conditions = 2%B to 50%B over 60 minutes, followed by a 50%-99% B in 6 minutes and then held for 3 minutes than 99%B to 2%B in 2 minutes and total run time of 90 minutes using Thermo Scientific Fusion Lumos mass spectrometer running in Data Independent Acquisition (DIA) mode.
Sagawa C.H.D., Zaini P.A., Assis R.M.d., Saxe H.J., Salemi M., Jacobson A., Phinney B.S., & Dandekar A.M. (2020). Deep learning neural network prediction method improves proteome profiling of vascular sap of grapevines during Pierce’s disease development.
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8

Peptide Separation and DIA Analysis

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Peptides were desalted and trapped on a Thermo PepMap trap and separated on an Easy-spray 100 µm x 25 cm C18 column using a Dionex Ultimate 3000 nUPLC at 200 nL/min. Solvent A = 0.1% formic acid, Solvent B = 100% Acetonitrile 0.1% formic acid. Gradient conditions = 2% B to 50% B over 60 minutes, followed by a 50%-99% B in 6 minutes and then held for 3 minutes than 99% B to 2% B in 2 minutes and total run time of 90 minutes using Thermo Scienti c Fusion Lumos mass spectrometer running in DIA mode. Six-gas phase fractionated (GPF) chromatogram library injections were made using staggered 4 Da isolation widows. GPF1 = 400-500 m/z, GPF2 = 500-600 m/z, GPF3 = 600-700 m/z, GPF4 = 700-800 m/z, GPF5 = 800-900 m/z, GPF6 = 900-1000 m/z, mass spectra were acquired using a collision energy of 35, resolution of 30 K, maximum inject time of 54 ms and a AGC target of 50K.
Each individual sample was run in DIA mode using the same settings as the chromatogram library runs except using staggered isolation windows of 12 Da in the m/z range 400-1000 m/z. DIA data was analyzed using Scaffold DIA v.2.0.0 (Proteome Software, Portland, OR, USA). Raw data les were converted to mzML format using ProteoWizard v.3.0.11748. 39 Total ion chromatograms can be found in S10 for CSF and S11 for Serum.
Lilley L.M., Sanche S., Moore S.C., Salemi M., Vu D.M., Iyer S., Hengartner N., & Mukundan H. (2022). Methods to Capture Proteomic and Metabolomic Signatures from Cerebrospinal Fluid and Serum of Healthy Individuals.
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