Ultimate 3000 rslcnano system

Manufactured by Thermo Fisher Scientific

Sourced in United States, Germany, Canada, United Kingdom, Japan, Netherlands

The UltiMate 3000 RSLCnano system is a high-performance liquid chromatography (HPLC) system designed for nano-scale separations. It features a low-volume, high-pressure nano-flow system capable of delivering mobile phases at precise flow rates, enabling the analysis of small sample volumes.

Automatically generated - may contain errors

Lab products found in correlation

Spelling variants of this product

Ultimate 3000 (1640 citations) Ultimate 3000 system (297 citations) UltiMate 3000 RSLCnano (138 citations) Dionex UltiMate 3000 RSLCnano system (110 citations) UltiMate 3000 RSLCnano LC system (61 citations) Ultimate 3000 RSLCnano HPLC system (49 citations) UltiMate 3000 RSLCnano UHPLC system (23 citations) UltiMate 3000 RSLCnano liquid chromatography system (15 citations) RSLCnano System (9 citations) Thermo Dionex UltiMate 3000 RSLCnano System (3 citations)

416 protocols using ultimate 3000 rslcnano system

Thylakoid Membrane Proteome Analysis

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

Isolated thylakoid membranes were subjected to filter-aided sample preparation as
described elsewhere (Wiśniewski et al.,
2009). The resulting peptides were analyzed by liquid chromatography–tandem mass
spectrometry (LC–MS/MS) performed using UltiMate 3000 RSLCnano system (Thermo Fisher
Scientific, Waltham, USA) on-line coupled with Orbitrap Elite hybrid spectrometer (Thermo
Fisher Scientific).
Bands with desired PSII supercomplexes separated by CN-PAGE were excised and after
washing procedures, each gel band was incubated with trypsin. LC–MS/MS analysis was
performed using UltiMate 3000 RSLCnano system (Thermo Fisher Scientific) on-line coupled
with Orbitrap Q Exactive HF-X spectrometer (Thermo Fisher Scientific). See the section
Supplemental Methods S1 for
full details regarding the analyses and data evaluation.

Ilíková I., Ilík P., Opatíková M., Arshad R., Nosek L., Karlický V., Kučerová Z., Roudnický P., Pospíšil P., Lazár D., Bartoš J, & Kouřil R. (2021). Towards spruce-type photosystem II: consequences of the loss of light-harvesting proteins LHCB3 and LHCB6 in Arabidopsis. Plant Physiology, 187(4), 2691-2715.

+ Open protocol

+ Expand

Quantitative LC-MS/MS Proteomics Workflow

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

Mass spectral data were acquired using LC-MS/MS, an Orbitrap Elite™ Hybrid Ion Trap-Orbitrap Mass Spectrometer coupled to an UltiMate™ 3000 RSLCnano System (Thermo Fisher, San Jose, CA, USA). The mass spectrometer was operated using XCalibur software (Thermo Fisher, San Jose, CA, USA). The mass range for MS scans was set to m/z 250–2000 at resolution 120,000 using FTMS analyzer. The MS/MS spectrum were selected from top seventh most abundant parent ions for each MS scan. The normalized collision energy for each MS/MS (CID) event using ITMS analyzer was set to 35%. Each peptide sample equivalent to 200 ng of undigested protein was subjected to EASY- Spray™ HPLC column (P/N ES802A, Thermo Fisher, San Jose, CA, USA) using an UltiMate™ 3000 RSLCnano System. The samples were loaded to EASY-SPRAY™ column using 2% acetonitrile (ACN) aqueous solution containing 0.1% formic acid. The separation was attained using a solvent gradient ramping from 2 to 40% aqueous ACN (0.1% formic acid) over 60 min at a flow rate of 300 nL/min. Each sample was analyzed in triplicate, providing three technical replicates per sample.

Chantaraamporn J., Champattanachai V., Khongmanee A., Verathamjamras C., Prasongsook N., Mingkwan K., Luevisadpibul V., Chutipongtanate S, & Svasti J. (2020). Glycoproteomic Analysis Reveals Aberrant Expression of Complement C9 and Fibronectin in the Plasma of Patients with Colorectal Cancer. Proteomes, 8(3), 26.

+ Open protocol

+ Expand

Label-free Proteomics of LEC Secretome

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

50 ml of LEC-conditioned was collected from five 10-cm dishes of cultured LECs and filtered through a 0.22μm pore membrane as mentioned above. LEC-conditioned media was further concentrated into 500uls using the Protein-Concentrate Kit (Millipore) according to the manufacture’s instruction. Protein concentration was then measured by the BCA protein assay (Thermo Fisher). Experiments were repeated three times and three biological samples were submitted to Northwestern Proteomics Core for untargeted quantitative proteomics analyses by Label-free Quantitative Proteomics: Briefly, samples were analyzed using an UltiMate™ 3000 RSLCnano system (ThemoFisher Scientific, CA) that is coupled with electrospray ionization (ESI) to a linear ion trap (LTQ) Orbitrap mass spectrometer (iLTQ-Orbitrap, ThermoFisher, CA). The resulting raw mass spectra from all three replicates were analyzed by the MaxQuant search engine (version 1.6.0.16) using UniprotKB human database with the allowance of up to 2 missed cleavages and precursor mass tolerance of 20 p.p.m. The secretome was acquired using software Scaffold 4 and annotated using Gene Ontology (GO), which assigns putative cellular compartmentalization, biological process and molecular functions.

Liu X., De la Cruz E., Gu X., Balint L., Oxendine-Burns M., Terrones T., Ma W., Kuo H.H., Lantz C., Bansal T., Thorp E., Burridge P., Jakus Z., Herz J., Cleaver O., Torres M, & Oliver G. (2020). Lymphoangiocrine signals promote cardiac growth and repair. Nature, 588(7839), 705-711.

+ Open protocol

+ Expand

Label-free Proteomics of LEC Secretome

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

+ Open protocol

+ Expand

Gel-based Proteomics of Arabidopsis

Cited 1 time

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

A. perfoliata somatic protein resolved on 1DE gels were subjected to GeLC proteomics. Each lane was cut into a series of 10 ‘bands’. Protein spots resolved from the purified GST were manually excised from the 2DE gels and used for classical in gel digestion. Protein bands and spots excised from the 1DE and 2DE gels were subjected to trypsin digestion prior to tandem mass spectrometry.
Gel pieces were de-stained and digested overnight in 10 ng/μL trypsin, as previously described (Rooney et al., 2022 (link)). Immediately prior to performing tandem mass spectrometry the dried peptides were re-suspended in 20 μL 0.1% v/v formic acid. For 2D SDS PAGE protein spots, the method of Duncan et al. (2018 (link)) was utilized for LC-MSMS. For whole A. perfoliata Orbitrap Fusion™ Tribrid™ mass spectrometer (Thermo Scientific™), with EASY-Spray™ Source, coupled to an UltiMate™ 3000 RSLCnano System (Thermo Scientific™) as per methods of Rooney et al. (2022 (link)).

Northcote H.M., Wititkornkul B., Cutress D.J., Allen N.D., Brophy P.M., Wonfor R.E, & Morphew R.M. (2024). A dominance of Mu class glutathione transferases within the equine tapeworm Anoplocephala perfoliata. Parasitology, 151(3), 282-294.

+ Open protocol

+ Expand

Virion Protein Analysis by Mass Spectrometry

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

To analyze virion proteins, CsCl-purified phage particles were mixed with a lysis buffer containing 62.5 mM Tris-HCl (pH 6.8), 5% 2-mercaptoethanol, 2% sodium dodecyl sulfate (SDS), 10% glycerol, and 0.01% bromophenol blue. The mixture was boiled for 10 min and separated via 12% SDS-PAGE. Protein bands were visualized using Coomassie blue staining. Proteins of interest were excised from the stained gels and subjected to in-gel digestion. The excised gel pieces were first reduced and then alkylated. The proteins were then digested with trypsin (Promega, Madison, WI, USA), and the resulting peptides were extracted from the gel pieces. The peptide mixture was analyzed using an UltiMate 3000 RSLCnano system coupled to a Q Exactive mass spectrometer (Thermo Fisher Scientific). The raw data obtained from the mass spectrometer were searched against a local database consisting of all possible peptide spectra deduced from the ECLFM1 genome sequence.

Ali S.F., Teh S.H., Yang H.H., Tsai Y.C., Chao H.J., Peng S.S., Chen S.C., Lin L.C, & Lin N.T. (2024). Therapeutic Potential of a Novel Lytic Phage, vB_EclM_ECLFM1, against Carbapenem-Resistant Enterobacter cloacae. International Journal of Molecular Sciences, 25(2), 854.

+ Open protocol

+ Expand

Optimized LC-MS/MS Proteomic Workflow

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

All samples were analyzed using Q Exactive HF-X mass spectrometer (Thermo, United States) and UltiMate 3000 RSLC nanosystem (Thermo, United States). The peptide was injected onto a self-made C18 column (75 μm × 25mm, Thermo, United States) in buffer A (2% acetonitrile and 0.1% Formic acid) and separated with a linear gradient of buffer B (80% acetonitrile and 0.1% Formic acid) at a flow rate of 300 nl/min. Through nanoelectrospray ionization and Q-Exactive HF-X quadrupole orbit rap mass spectrometer interface, the integrated column heater is set at 50°C, and the electrospray voltage is 1.8 kV. The tandem mass spectra of the first 20 ions were scanned with a full range of 350–1300 m/z, the isolation width was set to 1.6 Da, the resolution was 70K, and the MS/MS scan resolution was 17.5K. In all cases, one microscan was recorded using dynamic exclusion of 18 s.

Li B., Yang J., Gong Y., Xiao Y., Zeng Q., Xu K., Duan Y., He J., He J, & Ma H. (2021). Integrated Analysis of Liver Transcriptome, miRNA, and Proteome of Chinese Indigenous Breed Ningxiang Pig in Three Developmental Stages Uncovers Significant miRNA–mRNA–Protein Networks in Lipid Metabolism. Frontiers in Genetics, 12, 709521.

+ Open protocol

+ Expand

Quantitative Proteomics of Recombinant Streptomyces

Cited 1 time

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

Quantitative proteomics was used to analyse the expression of catechol dioxygenases and the expression profile of BGC4 in recombinant strains of Streptomyces sp. MBT84 as described previously^{45 (link)}. Briefly, the desalted peptide solution was separated on an UltiMate 3000 RSLCnano system (Thermo Scientific) set in a trap-elute configuration, coupled to QExactive HF (Thermo Scientific) mass spectrometer. The LC system used a Waters nanoEase M/Z Symmetry C₁₈ trap column (5 µm, 100 Å, 180 µm × 20 mm) for peptide loading/retention, and Waters nanoEase M/Z HSS T3 C₁₈ analytical column (1.8 µm, 100 Å, 75 µm × 250 mm) for peptide separation. The MS was operated in positive mode with data-dependent acquisition and default charge of 2. Raw LC-MS/MS files were analysed using MaxQuant software (v1.6.17.0)^{57 (link)} with label-free quantification (LFQ) method applied. Proteins were considered significantly altered in expression when FDR-adjusted p < 0.1 were obtained.

van Bergeijk D.A., Elsayed S.S., Du C., Santiago I.N., Roseboom A.M., Zhang L., Carrión V.J., Spaink H.P, & van Wezel G.P. (2022). The ubiquitous catechol moiety elicits siderophore and angucycline production in Streptomyces. Communications Chemistry, 5, 14.

+ Open protocol

+ Expand

HPLC Analysis of Glutathione Redox Status

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

The HPLC analysis
of GSH and GSSG was performed using a Hitachi Primaide instrument
on a C18 column (XBridge Peptide BEH C18 column from Waters, 4.6 mm
× 150 mm, pore size 300 Å, particle size 3.5 μm) using
0.1% aqueous TFA (solvent A) and 90% CH₃CN/0.1% TFA in
water (solvent B) with a linear gradient from 5 to 10% solvent B in
7 min. The attribution of the peaks was achieved by comparison with
a solution containing GSH or GSSG only and via LC-MS spectra that
were recorded using an LCQ Fleet ion trap mass spectrometer (Thermo
Fischer) coupled to a Ultimate3000 RSLCnano system equipped with an
ACQUITY UPLC BEH C18 column (130 Å, 1.7 μm, 1.0 mm ×
150 mm).

Falcone E., Ritacca A.G., Hager S., Schueffl H., Vileno B., El Khoury Y., Hellwig P., Kowol C.R., Heffeter P., Sicilia E, & Faller P. (2022). Copper-Catalyzed Glutathione Oxidation is Accelerated by the Anticancer Thiosemicarbazone Dp44mT and Further Boosted at Lower pH. Journal of the American Chemical Society, 144(32), 14758-14768.

+ Open protocol

+ Expand

Peptide Identification in GTR Hydrolysates

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

To identify peptides in GTR hydrolysates, an UltiMate 3000 RSLC nano system coupled to a Q‐Exactive Orbitrap HF‐X mass spectrometer (Thermo Fisher Scientific) was used in direct injection mode, as described previously (Lee et al., 2022 (link)). GTR hydrolysates containing peptides (3 μg) were loaded onto a trap column (internal diameter, I.D. 75 μm × 2 cm, packed with Acclaim PepMap 100 C18, 3 μm, 100 Å; Thermo Fisher Scientific) and eluted onto an analytical column (I.D. 75 μm × 50 cm, packed with PepMap RSLC C18, 2 μm; Thermo Fisher Scientific) at a flow rate of 0.27 μl/min. The mobile phase consisted of 0.1% (v/v) formic acid (FA) in water (solvent A) and 0.1% (v/v) FA in acetonitrile (ACN) (solvent B). MS analysis of peptide eluents was performed on a Q‐Exactive Orbitrap HF‐X mass spectrometer in the positive‐ion mode. The normalized collision energy was 27% for the MS2 analysis.

Lee J., Hong H., Lee J., Hong Y., Hwang H.W., Jin H., Shim H., Hong Y., Park W., Chung J, & Lee D. (2022). Valorization of leftover green tea residues through conversion to bioactive peptides using probiotics‐aided anaerobic digestion. Microbial Biotechnology, 16(2), 418-431.

+ 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!