Acclaim pepmap 100 pre column

Manufactured by Thermo Fisher Scientific

Sourced in United States

The Acclaim PepMap 100 pre-column is a high-performance liquid chromatography (HPLC) column designed for sample clean-up and analyte enrichment prior to separation and analysis. The pre-column features a silica-based stationary phase with a pore size of 100 Angstroms and particle size of 3 micrometers, providing efficient sample preparation for complex mixtures.

Automatically generated - may contain errors

Lab products found in correlation

16 protocols using acclaim pepmap 100 pre column

Quantitative TMT Proteomics Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols

The mass spectrometric quantitative analysis of 1 μL of the re-dissolved TMT-labeled peptide fractions was performed on an Orbitrap Fusion Lumos mass spectrometer coupled with an EASY-nLC 1200 nano-UPLC system equipped with an Acclaim™ PepMap™ 100 pre-column (20 mm × 75 μm, 3 μm) and an Acclaim™ PepMap™ RSLC C18 analytical column (150 mm × 75 μm, 2 μm) (Thermo Fisher Scientific, Waltham, MA, USA). The UPLC gradient started with 2% B and increased to 7% at 7 min, then to 20% at 69 min, 35% at 90 min and sharply to 95% within 5 min, remained for 4 min, and finally decreased to 2% within 8 min and remained for 3 min.
The voltage of electrospray ionization (ESI) was set as 2200 V, the ion transfer tube temperature was 320 °C. For primary mass spectrometry analysis, an Orbitrap detector was operated with a mass resolution of 120,000 and a scanning range from 350 to 1700 m/z. The Orbitrap was also used as the detector of MS/MS with a mass resolution of 15,000, and of MS³ with a resolution of 50,000 and a scanning range of 100–200 m/z. The HCD fragmentation cell ran with a collision energy of 23% for the second mass spectrometry (MS/MS) analysis, and with a collision energy of 60% for the third mass spectrometry (MS³) analysis.

Tian X., Gu L., Zeng F., Liu X., Zhou Y., Dou Y., Han J., Zhao Y., Zhang Y., Luo Q, & Wang F. (2024). Strophanthidin Induces Apoptosis of Human Lung Adenocarcinoma Cells by Promoting TRAIL-DR5 Signaling. Molecules, 29(4), 877.

+ Open protocol

+ Expand

Nano-LC-MS/MS Workflow for Peptide Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols

An aliquot of each sample was loaded onto a trap column (Acclaim PepMap 100 pre-column, 75 μm × 2 cm, C18, 3 μm, 100 Å, Thermo Scientific) connected to an analytical column (EASY-Spray column, 50 m × 75 μm ID, PepMap RSLC C18, 2 μm, 100 Å, Thermo Scientific) using the autosampler of an Easy nLC 1000 (Thermo Scientific) with solvent A consisting of 2% acetonitrile in 0.5% acetic acid and solvent B consisting of 80% acetonitrile in 0.5% acetic acid. The peptide mixture was gradient eluted into the QExactive mass spectrometer (Thermo Scientific) using the following gradient: a 5%-23% solvent B in 100 min, 23% -34% solvent B in 20 min, 34% -56% solvent B in 10 min, followed by 56%- 100% solvent B in 20 min. The full scan was acquired with a resolution of 70,000 (@ m/z 200), a target value of 1e6 and a maximum ion time of 120 ms. After each full scan 10 HCD MS/MS scans were acquired using the following parameters: resolution 35,000 (@m/z 200), isolation window of 1.5 m/z, target value of 1e5, maximum ion time of 250 ms, normalized collision energy (NCE) of 30, and dynamic exclusion of 30 s.

Joshi A., Mahmoud S.A., Kim S.K., Ogdahl J.L., Lee V.T., Chien P, & Yildiz F.H. (2020). c-di-GMP inhibits LonA-dependent proteolysis of TfoY in Vibrio cholerae. PLoS Genetics, 16(6), e1008897.

+ Open protocol

+ Expand

UPLC-MS/MS Proteome Analysis Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols

Dried samples were resuspended in 15 µl 0.1% FA/5% ACN before being injected (5 μL) and separated on an Ultimate 3000 UPLC system (Dionex, Thermo Scientific) equipped with an Acclaim PepMap 100 pre-column (C18 3 μm–100 Å, Thermo Scientific) and a C18 PepMap RSLC (2 μm, 50 μm-15 cm, Thermo Scientific) using a linear gradient (300 nL/min) of 0–4% buffer B (80% ACN, 0.08% FA) in 3 min, 4–10% B in 7 min, 10–35% in 25 min, 35–38% in 5 min, 38–40% in 2 min, 40–65% in 5 min, 65–95% in 1 min, 95% for 9 min, 95–5% in 1 min, 5% for 9 min.
The Q Exactive Orbitrap mass spectrometer (Thermo Scientific) was operated in positive ion mode using data-dependent acquisition with a survey MS scan at a resolution of 70,000 (FWHM at m/z 200), followed by MS/MS scans (resolution 17,500) of the top ten most intense peaks with +2, +3, +4, and +5 charged ions above a threshold ion count of 16,000 using normalized collision energy (NCE) of 25 eV with an isolation window of 2.0 m/z, apex trigger of 5-15 s and dynamic exclusion of 30 s. All data were acquired with Xcalibur 3.1.66.10 software (Thermo Scientific).
Measurements were taken from distinct samples.
MS data are available via ProteomeXchange with identifier PXD038849.

Frans G., Dillaerts D., Dehaemers T., Van Elslande J., De Leeuw J., Boon L., Maes W., Callewaert N., Calcoen B., Ancheva L., Cockx M., Geukens N., Arat K., Derua R., Vermeersch P., Carpentier S.C, & Bossuyt X. (2023). Complementarity determining regions in SARS-CoV-2 hybrid immunity. Frontiers in Immunology, 14, 1050037.

+ Open protocol

+ Expand

Proteome Profiling using Orbitrap Lumos

Check if the same lab product or an alternative is used in the 5 most similar protocols

An aliquot of each final fraction was loaded onto a trap column (Acclaim® PepMap 100 pre-column, 75 μm × 2 cm, C18, 3 μm, 100 Å, Thermo Scientific) connected to an analytical column (EASY-Spray column, 50 m × 75 μm ID, PepMap RSLC C18, 2 μm, 100 Å, Thermo Scientific) using the autosampler of an Easy nLC 1000 (Thermo Scientific) with solvent A consisting of 2% acetonitrile in 0.5% acetic acid and solvent B consisting of 80% acetonitrile in 0.5% acetic acid. The peptide mixture was gradient eluted into the Orbitrap Lumos Fusion mass spectrometer (Thermo Scientific) using the following gradient: 5%–5% solvent B in 100 min, 23% – 34% solvent B in 20 min, 34% – 56% solvent B in 10 min, followed by 56%- 100% solvent B in 20 min. Full scans were acquired with a resolution of 60,000 (@ m/z 200), a target value of 4e5 and a maximum ion time of 50 ms. After each full scan the most intense ions above 5e4 were selected for fragmentation with HCD using the “Top Speed” algorithm. The MS/MS were acquired in the Orbitrap with a resolution of 60,000 (@ m/z 200), isolation window of 1.5 m/z, target value of 1e5, maximum ion time of 60 ms, normalized collision energy (NCE) of 35, and dynamic exclusion of 30 s.

Kleffman K., Levinson G., Rose I.V., Blumenberg L.M., Shadaloey S.A., Dhabaria A., Wong E., Galán-Echevarría F., Karz A., Argibay D., Von Itter R., Floristán A., Baptiste G., Eskow N.M., Tranos J.A., Chen J., Vega y Saenz de Miera E.C., Call M., Rogers R., Jour G., Wadghiri Y.Z., Osman I., Li Y.M., Mathews P., DeMattos R., Ueberheide B., Ruggles K.V., Liddelow S.A., Schneider R.J, & Hernando E. (2022). Melanoma-secreted Amyloid Beta Suppresses Neuroinflammation and Promotes Brain Metastasis. Cancer discovery, 12(5), 1314-1335.

+ Open protocol

+ Expand

Intact Glycopeptides Analysis Protocol

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

One microgram of glycopeptides was separated on an EASY-nLC™ 1200 instrument (Thermo Fisher Scientific, Germany) with the use of Acclaim PepMap100 precolumn (2 cm, 75 µm i.d., 3 µm) and Acclaim PepMap100 separating column (50 cm, 75 µm i.d., 3 µm) operating at 300 nL/min. The mobile phase A (0.1% FA) and mobile phase B (0.1% FA / 80% ACN) with a flow rate of 200 nL/min. The parameters used for intact glycopeptides analysis were the same as previously described [22 (link), 23 (link)].

Yu H., Li M., Shu J., Dang L., Wu X., Wang Y., Wang X., Chang X., Bao X., Zhu B., Ren X., Chen W, & Li Y. (2023). Characterization of aberrant glycosylation associated with osteoarthritis based on integrated glycomics methods. Arthritis Research & Therapy, 25, 102.

+ Open protocol

+ Expand

Tandem Mass Spectrometry of Peptides

Check if the same lab product or an alternative is used in the 5 most similar protocols

An EASY-nLC 1000 liquid chromatography system interfaced with a Q Exactive mass spectrometer (Thermo Scientific) via a nanospray flex ion source was employed for the mass spectrometric analyses. Peptides were loaded onto an Acclaim PepMap100 pre-column (75 μm × 2 cm, Thermo Scientific) connected to an Acclaim PepMap RSLC (50 μm × 15 cm, Thermo Scientific) analytical column. A 2 to 40% acetonitrile in 0.1% formic acid linear gradient, at a flow rate of 300 nl min⁻¹ over 45 min, was used to elute peptides from the columns. The mass spectrometer was operated in positive ion mode. Full MS scans were acquired from m/z 300 to 1850 with a resolution of 70,000 at m/z 200. The ten most intense ions were fragmented by higher energy C-trap dissociation with normalized collision energy of 28. MS/MS spectra were recorded with a resolution of 17,500 at m/z 200. The maximum ion injection time was 120 ms for both survey and MS/MS scans, whereas automatic gain control target values of 3 × 10⁶ and 5 × 10⁵ were used for survey and MS/MS scans, respectively. Dynamic exclusion was applied for 45 s to avoid repeated sequencing of peptides. Singly charged ions or ions with unassigned charge state were also excluded from MS/MS. Data were acquired using Xcalibur software (Thermo Scientific).

Ramírez J., Morales M., Osinalde N., Martínez-Padrón I., Mayor U, & Ferrús A. (2021). The ubiquitin ligase Ariadne-1 regulates neurotransmitter release via ubiquitination of NSF. The Journal of Biological Chemistry, 296, 100408.

+ Open protocol

+ Expand

Proteomics Workflow for Peptide Quantification

Check if the same lab product or an alternative is used in the 5 most similar protocols

The samples, dissolved in 2% acetonitrile/0.2% TFA, were injected to the LC-MS/MS in a volume of 9 μl (Q Exactive, ThermoScientific). Mobile phase A was 0.1% formic acid in water, and mobile phase B was acetonitrile with 0.1% formic acid. The peptides were eluted by a 120 min long gradient; 0–30% B from 0–100 min and 30–65% B from 100–120 min at a flow rate of 300 nl/min. The analytical column was a NANO-HPLC capillary C18 column, 0.075×150 mm (Nikkyo Technos) and the trap column was an Acclaim® PepMap100 pre-column, 100 μm×2 cm (Thermo Fisher Scientific). Peptide selection was set at m/z 350–1800. The combined resulting mass spectra data from the four fractions were subjected to Proteome Discoverer (Ver.1.4) with the MASCOT search engine (Ver. 2.5.1) against SwissProt database 2015_04 with search criteria; ¹⁸O incomplete labeling (Heavy+Medium)/Light. The median ratio was set to 1 for each analysis.

Schedin-Weiss S., Nilsson P., Sandebring-Matton A., Axenhus M., Sekiguchi M., Saito T., Winblad B., Saido T, & Tjernberg L.O. (2020). Proteomics Time-Course Study of App Knock-In Mice Reveals Novel Presymptomatic Aβ42-Induced Pathways to Alzheimer’s Disease Pathology. Journal of Alzheimer's Disease, 75(1), 321-335.

+ Open protocol

+ Expand

Glycopeptide Analysis by Orbitrap Fusion Lumos

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

The samples of TMT-labeled peptide and intact glycopeptide were separated in an Easy-nLCTM 1200 system (Thermo Fisher Scientific) by using Acclaim PepMap100 precolumn (2 cm, 75 μm i.d., 3 μm) and Acclaim Pepmap100 separation column (50 cm, 75 μm i.d., 3 μm). The mobile-phase flow rate was 200 nL/min and consisted of 0.1% formic acid in water (A) and 0.1% formic acid in 80% acetonitrile (B). For the analysis with five fragmentation energies, the gradient profile was set as follows: 3–7% B for 3 min, 7–35% B for 91 min, 35–68% B for 19 min, 68–99% B for 4 min, and equilibrated in 100% B for 13 min. MS analysis was performed using an Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientific, Germany). The spray voltage was set at 2400 V. Orbitrap spectra (AGC 4×10⁵) were collected from 350 m/z to 2000 m/z at a resolution of 120 K followed by oxonium ions triggered by data-dependent higher-energy collisional dissociation (HCD) MS/MS (at a resolution of 50 K, collision energy 20%, AGC 5×10⁴, and collision energy 37%, AGC 2×10⁵) using an isolation width of 1.6 Da. Charge state screening (2–7) was enabled to reject unassigned and singly charged ions. Polypeptides with a scanning range of 110–3000 m/z were selected for MS/MS collection. A dynamic exclusion time of 5 s was used to discriminate against previously selected ions.22 (link)

Wang H., Shi Y., Ma J., Wang W., Gao J., Zhao L., Zhao T, & Ding G. (2023). Integrated Proteomic and N-Glycoproteomic Profiling of Placental Tissues of Patients with Preeclampsia. International Journal of Women's Health, 15, 59-68.

+ Open protocol

+ Expand

Peptide Identification Pipeline for Oral Pathogens

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

The peptide samples (5 µL of each sample) were digested and subsequently injected for UPLC separation by an Ultimate 3000 UPLC System (Dionex, Thermo Fisher Scientific, Waltham, USA), using an Acclaim PepMap100 pre-column (C18 3µm-100 Å, Thermo Fisher Scientific, Waltham, USA) and a C18 PepMap RSLC (2 μm, 50 μm-15 cm, Thermo Fisher Scientific, Waltham, USA) using a linear gradient (300 μL/min) of 0–4% buffer B (80% ACN, 0.08% FA) for 3 min, 4–10% B for 12 min, 10–35% for 20 min, 35–65% for 5 min, 65–95% for 1 min, 95% for 10 min, 95–5% for 1 min, and 5% for 10 min. The operational settings of the mass spectrometer and data acquisition procedure were identical to those described earlier by Khodaparast et al.^{55 (link)}. With the purpose of identification, all raw data were converted into mgf.files using Proteome Discover version 1.4 (Thermo Fisher Scientific, Waltham, USA) and processed with MASCOT version 2.2.06 (Matrix Science Ltd, London, UK) against the Uniprot A. actinomycetemcomitans, F. nucleatum, P. gingivalis or P. intermedia database. The parameters used to search with MASCOT are described elsewhere^{55 (link)}. MASCOT results were imported to Scaffold (version 3.6.3). The parameters used in Scaffold for protein identification were retaining proteins with 99% confidence and containing at least two identified peptides with a confidence level of 95%.

Verspecht T., Rodriguez Herrero E., Khodaparast L., Khodaparast L., Boon N., Bernaerts K., Quirynen M, & Teughels W. (2019). Development of antiseptic adaptation and cross-adapatation in selected oral pathogens in vitro. Scientific Reports, 9, 8326.

+ Open protocol

+ Expand

Nano-LC-MS/MS Proteomics Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols

1 μg of each sample was loaded onto a trap column (Acclaim® PepMap 100 pre-column, 75 μm × 2 cm, C18, 3 μm, 100 Å, Thermo Scientific) connected to an analytical column (EASY-Spray column, 50 μm × 75 μm ID, PepMap RSLC C18, 2 μm, 100 Å, Thermo Scientific) using the autosampler of an Easy nLC 1000 (Thermo Scientific) with solvent A consisting of 2% acetonitrile in 0.5% acetic acid and solvent B consisting of 80% acetonitrile in 0.5% acetic acid. The peptide mixture was gradient eluted into the Orbitrap QExactive HF-X Mass Spectrometer (Thermo Scientific) using the following gradient: a 5%−35% solvent B in 120 min, 35% −45% solvent B in 10 min, followed by 45%- 100% solvent B in 20 min. The full scan was acquired with a resolution of 60,000 (@ m/z 200), a target value of 3e6 and a maximum ion time of 45 ms. Following each full MS scan, twenty data-dependent MS/MS spectra were acquired. The MS/MS spectra were collected with a resolution of 15,000, an AGC target of 1e5, maximum ion time of 120ms, one microscan, 2m/z isolation window, fixed first mass of 150 m/z, dynamic exclusion of 30 sec, and Normalized Collision Energy (NCE) of 27.

Keller M.D., Ching K.L., Liang F.X., Dhabaria A., Tam K., Ueberheide B.M., Unutmaz D., Torres V.J, & Cadwell K. (2020). Decoy exosomes provide protection against bacterial toxins. Nature, 579(7798), 260-264.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!