Log In Sign up
The largest database of trusted experimental protocols

Dionex ultimate 3000 rapid separation nanolc

Manufactured by Thermo Fisher Scientific
Visit Supplier

The Dionex UltiMate 3000 Rapid Separation nanoLC is a high-performance liquid chromatography (HPLC) system designed for analytical-scale separations. It features a modular design and supports a wide range of application areas, including proteomics, metabolomics, and small-molecule analysis.

Automatically generated - may contain errors

Lab products found in correlation

Q exactive hf hybrid quadrupole orbitrap mass spectrometer, by Thermo Fisher Scientific (5 mentions) Picochip column, by New Objective (3 mentions) C18 beads, by New Objective (3 mentions) Orbitrap elite mass spectrometer, by Thermo Fisher Scientific (2 mentions) Reprosil pur beads, by New Objective (2 mentions) Picochip, by New Objective (1 mentions) Scaffold v 5, by Proteome Software (1 mentions) Mascot search engine, by Matrix Science (1 mentions) Streptavidin beads, by Santa Cruz Biotechnology (1 mentions)

7 protocols using dionex ultimate 3000 rapid separation nanolc

1

Quantitative Proteomic Analysis of Peptide Samples

Check if the same lab product or an alternative is used in the 5 most similar protocols
The obtained peptides were analyzed by liquid chromatography with tandem mass spectrometry (LC-MS/MS) using a Dionex UltiMate 3000 Rapid Separation nanoLC and a Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer (Thermo Fisher). Samples were loaded onto a house-packed C18 column and separated with a 5 to 40% gradient of solvent (0.1% FA in ACN) for 120 min by an analytical column (PicoChip, New Objective, Inc.). MS/MS spectra were searched against the SwissProt Mus musculus database using Mascot search engine (Matrix Science; version 2.7.0.1). All searches included carbamidomethyl Cys as a fixed modification and oxidized Met; deamidated Asn and Gln; and acetylated N-term as variable modifications. The search result was visualized by Scaffold v 5.0.1 (Proteome Software, Inc.). A 1% false discovery rate of the protein with a minimum of two unique peptides was identified. Statistical analysis, specifically, a Fisher’s exact test with a Benjamini–Hochberg multiple test correction, was performed for comparison between 200-SNA and 150-SNA groups (n = 4 and 3 samples per group, respectively).
Teplensky M.H., Distler M.E., Kusmierz C.D., Evangelopoulos M., Gula H., Elli D., Tomatsidou A., Nicolaescu V., Gelarden I., Yeldandi A., Batlle D., Missiakas D, & Mirkin C.A. (2022). Spherical nucleic acids as an infectious disease vaccine platform. Proceedings of the National Academy of Sciences of the United States of America, 119(14), e2119093119.
+ Open protocol
+ Expand
2

BioID Screening for Proximal Interacting Proteins

Check if the same lab product or an alternative is used in the 5 most similar protocols
BioID is a novel method to screen for interacting protein partners that are in close proximity in living cells. BioID was performed as previously described (33 (link), 34 ). Briefly, HEKs were transduced with a fusion of a promiscuous biotin ligase (BirA*) to FIH-1 (a bait), or an empty vector LZRS. These cells were used to generate 3-D raft cultures as previously described (23 (link)). At day 9, rafts were treated with biotin daily for 3 days. At day 12, rafts were harvested for proteins. Endogenous binding partner proteins with FIH-1 were biotinylated. These biotinylated proteins were isolated using Streptavidin beads (Santa Cruz Biotechnology, Texas, USA) under a constringent condition for identification by mass spectrometry without loss of weaker binding partners. Peptides were analyzed by LC-MS/MS using a Dionex UltiMate 3000 Rapid Separation nanoLC and a Q Exactive™ HF Hybrid Quadrupole-Orbitrap™ Mass Spectrometer (ThermoFisher Scientific). Trap column: 150 μm x 3 cm in-house packed with 3 um C18 beads. Analytical column: 75 um x 10.5 cm PicoChip column packed with 1.9 um C18 beads (New Objectives). Data were analyzed and exported using Scaffold.4.8.2 software.
Kaplan N., Dong Y., Wang S., Yang W., Park J.K., Wang J., Fiolek E., White B.P., Chandel N.S., Peng H, & Lavker R.M. (2019). FIH-1 engages novel binding partners to positively influence epithelial proliferation via p63. FASEB journal : official publication of the Federation of American Societies for Experimental Biology, 34(1), 525-539.
+ Open protocol
+ Expand
3

Peptide Identification by LC-MS/MS

Check if the same lab product or an alternative is used in the 5 most similar protocols
Peptides were analyzed by LC-MS/MS using a Dionex UltiMate 3000 Rapid Separation nanoLC and a Q Exactive™ HF Hybrid Quadrupole-Orbitrap™ Mass Spectrometer (Thermo Fisher Scientific). Approximately 1 μg of peptide samples was loaded onto the trap column, which was 150 μm × 3 cm in-house packed with 3 μm C18 beads. The analytical column was a 75 μm × 10.5 cm PicoChip column packed with 3 μm C18 beads (New Objective, Inc.). The flow rate was kept at 300 nL/min. Solvent A was 0.1% FA in water and Solvent B was 0.1% FA in ACN. The peptide was separated on a 120-min analytical gradient from 5% ACN/0.1% FA to 40% ACN/0.1% FA. The mass spectrometer was operated in data-dependent mode. The source voltage was 2.10 kV and the capillary temperature was 320 °C. MS1 scans were acquired from 300–2000 m/z at 60,000 resolving power and automatic gain control (AGC) set to 3 × 106. The top 15 most abundant precursor ions in each MS1 scan were selected for fragmentation. Precursors were selected with an isolation width of 2 Da and fragmented by higher-energy collisional dissociation (HCD) at 30% normalized collision energy in the HCD cell. Previously selected ions were dynamically excluded from re-selection for 20 seconds. The MS2 AGC was set to 1 × 105. All samples were run in duplicate.
Henning N.F., LeDuc R.D., Even K.A, & Laronda M.M. (2019). Proteomic analyses of decellularized porcine ovaries identified new matrisome proteins and spatial differences across and within ovarian compartments. Scientific Reports, 9, 20001.
+ Open protocol
+ Expand
4

Peptide Analysis by Nano-LC-MS/MS

Check if the same lab product or an alternative is used in the 5 most similar protocols
Peptides were analyzed by LC-MS/MS using a Dionex UltiMate 3000 Rapid Separation nanoLC coupled to a Orbitrap Elite Mass Spectrometer (Thermo Fisher Scientific Inc, San Jose, CA). Samples were loaded onto the trap column, which was 150 μm x 3 cm in-house packed with 3 um ReproSil-Pur® beads. The analytical column was a 75 um x 10.5 cm PicoChip column packed with 3 um ReproSil-Pur® beads (New Objective, Inc. Woburn, MA). The flow rate was kept at 300nL/min. Solvent A was 0.1% FA in water and Solvent B was 0.1% FA in ACN. The peptide was separated on a 120-min analytical gradient from 5% ACN/0.1% FA to 40% ACN/0.1% FA. MS1 scans were acquired from 400–2000m/z at 60,000 resolving power and automatic gain control (AGC) set to 1×106. The 15 most abundant precursor ions in each MS1 scan were selected for fragmentation by collision-induced dissociation (CID) at 35% normalized collision energy in the ion trap. Previously selected ions were dynamically excluded from re-selection for 60 seconds. Samples were analyzed in biological triplicates.
Aoi Y., Takahashi Y.H., Shah A.P., Iwanaszko M., Rendleman E.J., Khan N.H., Cho B.K., Ah Goo Y., Ganesan S., Kelleher N.L, & Shilatifard A. (2021). SPT5 stabilization of promoter-proximal RNA polymerase II. Molecular cell, 81(21), 4413-4424.e5.
+ Open protocol
+ Expand
5

Peptide Analysis by LC-MS/MS

Check if the same lab product or an alternative is used in the 5 most similar protocols
Peptides were analyzed by LC-MS/MS using a Dionex UltiMate 3000 Rapid Separation nanoLC and a Q Exactive™ HF Hybrid Quadrupole-Orbitrap™ Mass Spectrometer (Thermo Fisher Scientific Inc, San Jose, CA). Approximately 2 μg of peptide samples was loaded onto the trap column, which was 150 μm × 3 cm in-house packed C18 beads. The analytical column was a 75 μm × 10.5 cm PicoChip column packed with 3 μm C18 beads (New Objective, Inc. Woburn, MA). The flow rate was kept at 300 nL/min. Solvent A was 0.1% FA in water and Solvent B was 0.1% FA in ACN. The peptide was separated on a 120-min analytical gradient from 5% ACN/0.1% FA to 40% ACN/0.1% FA. The mass spectrometer was operated in data-dependent mode. The source voltage was 2.40 kV. MS1 scans were acquired from 300 to 2000 m/z at 60,000 resolving power and automatic gain control (AGC) set to 3 × 106. The top 20 most abundant precursor ions in each MS1 scan were selected for fragmentation. Precursors were selected with an isolation width of 2 m/z and fragmented by Higher-energy collisional dissociation (HCD) at 30% normalized collision energy in the HCD cell. Previously selected ions were dynamically excluded from re-selection for 20 s. The MS2 minimum AGC was set to 1 × 103. Data was acquired in technical duplicates.
Mondal C., Gacha-Garay M.J., Larkin K.A., Adikes R.C., Di Martino J.S., Chien C.C., Fraser M., Eni-aganga I., Agullo-Pascual E., Cialowicz K., Ozbek U., Naba A., Gaitas A., Fu T.M., Upadhyayula S., Betzig E., Matus D.Q., Martin B.L, & Bravo-Cordero J.J. (2022). A proliferative to invasive switch is mediated by srGAP1 downregulation through the activation of TGF-β2 signaling. Cell reports, 40(12), 111358.
+ Open protocol
+ Expand
6

Peptide Identification by LC-MS/MS

Check if the same lab product or an alternative is used in the 5 most similar protocols
Peptides were analyzed by LC-MS/MS using a Dionex UltiMate 3000 Rapid Separation nanoLC coupled to the Orbitrap Elite Mass Spectrometer (Thermo Fisher Scientific Inc, San Jose, CA). Samples were loaded onto the trap column, which was 150 μm x 3 cm in-house packed with 3 um ReproSil-Pur® beads. The analytical column was a 75 um x 10.5 cm PicoChip column packed with 3 um ReproSil-Pur® beads (New Objective, Inc. Woburn, MA). The flow rate was kept at 300nL/min. Solvent A was 0.1% FA in water and Solvent B was 0.1% FA in ACN. The peptide was separated on a 120-min analytical gradient from 5% ACN/0.1% FA to 40% ACN/0.1% FA. MS1 scans were acquired from 400–2000m/z at 60,000 resolving power and automatic gain control (AGC) set to 1×106. The 15 most abundant precursor ions in each MS1 scan were selected for fragmentation by collision-induced dissociation (CID) at 35% normalized collision energy in the ion trap. Previously selected ions were dynamically excluded from re-reselection for 60 seconds. Samples were analyzed in 6 or 3 biological replicates.
Aoi Y., Shah A.P., Ganesan S., Soliman S.H., Cho B.K., Goo Y.A., Kelleher N.L, & Shilatifard A. (2022). SPT6 functions in transcriptional pause/release via PAF1C recruitment. Molecular cell, 82(18), 3412-3423.e5.
+ Open protocol
+ Expand
7

Peptide Analysis by LC-MS/MS

Check if the same lab product or an alternative is used in the 5 most similar protocols
Peptides were analyzed by LC-MS/MS using a Dionex UltiMate 3000 Rapid Separation nanoLC and a Q Exactive™ HF Hybrid Quadrupole-Orbitrap™ Mass Spectrometer (Thermo Fisher Scientific Inc, San Jose, CA). Approximately 2 μg of peptide samples was loaded onto the trap column, which was 150 μm × 3 cm in-house packed C18 beads. The analytical column was a 75 μm × 10.5 cm PicoChip column packed with 3 μm C18 beads (New Objective, Inc. Woburn, MA). The flow rate was kept at 300 nL/min. Solvent A was 0.1% FA in water and Solvent B was 0.1% FA in ACN. The peptide was separated on a 120-min analytical gradient from 5% ACN/0.1% FA to 40% ACN/0.1% FA. The mass spectrometer was operated in data-dependent mode. The source voltage was 2.40 kV. MS1 scans were acquired from 300 to 2000 m/z at 60,000 resolving power and automatic gain control (AGC) set to 3 × 106. The top 20 most abundant precursor ions in each MS1 scan were selected for fragmentation. Precursors were selected with an isolation width of 2 m/z and fragmented by Higher-energy collisional dissociation (HCD) at 30% normalized collision energy in the HCD cell. Previously selected ions were dynamically excluded from re-selection for 20 s. The MS2 minimum AGC was set to 1 × 103. Data was acquired in technical duplicates.
Mondal C., Gacha-Garay M.J., Larkin K.A., Adikes R.C., Di Martino J.S., Chien C.C., Fraser M., Eni-aganga I., Agullo-Pascual E., Cialowicz K., Ozbek U., Naba A., Gaitas A., Fu T.M., Upadhyayula S., Betzig E., Matus D.Q., Martin B.L, & Bravo-Cordero J.J. (2022). A proliferative to invasive switch is mediated by srGAP1 downregulation through the activation of TGF-β2 signaling. Cell reports, 40(12), 111358.
+ 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?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!