4000 series explorer software

Manufactured by Thermo Fisher Scientific

Sourced in United States

The 4000 Series Explorer software is a data acquisition and analysis platform designed for use with Thermo Fisher Scientific instrumentation. It provides a user-friendly interface for controlling and monitoring the operation of compatible devices, as well as tools for processing and interpreting the data collected.

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Lab products found in correlation

4800 plus maldi tof tof analyzer, by Thermo Fisher Scientific (2 mentions) Data explorer software, by Thermo Fisher Scientific (2 mentions) Milli q, by Merck Group (1 mentions) Imagequant software, by GE Healthcare (1 mentions) 4800 proteomics analyzer maldi tof tof mass spectrometer, by Thermo Fisher Scientific (1 mentions) 4800 proteomics analyzer, by Thermo Fisher Scientific (1 mentions) 4800 maldi tof tof analyzer, by Thermo Fisher Scientific (1 mentions) Data explorer software version 4, by Thermo Fisher Scientific (1 mentions) Proteinpilot, by AB Sciex (1 mentions) Ettan digester, by GE Healthcare (1 mentions) 4800 maldi tof tof mass spectrometer, by Thermo Fisher Scientific (1 mentions) Mascot distiller, by Matrix Science (1 mentions)

10 protocols using 4000 series explorer software

Investigating Peptide Binding on Metal Surfaces

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Ti and Ti6Al4V surfaces were incubated in a 100-µM solution of SVSVGMKPSPRP peptide (MBP-1) or WDPPTLKRPVSP peptide (MBP-2) for 2 h. The samples were rinsed thoroughly, either with a hydrophilic solution: ultra clean water (Milli-Q; Merck Millipore, Darmstadt, Germany), a hydrophobic solution: acetonitrile 100% (Sigma—Aldrich St. Louis, MO, United States) or an ionic solution (NaCl, 1 M). The presence of the peptides on the dry surfaces was identified with MALDI TOF/TOF spectrometry. Samples were analyzed using a 4,800 Plus MALDI-tandem time-of-flight system (MALDI-TOF/TOF) Proteomics Analyzer (Applied Bio systems, Foster City, CA, United States) in positive reflector ion mode using a 20-kV acceleration voltage. The YAG laser was operated at a 200-Hz firing rate with a wavelength of 355 nm. Mass spectrometry spectra were acquired for each sample using 1,500 laser shots. All acquired spectra of the samples were processed using the 4,000 Series Explorer TM software (Applied Bio systems, Foster City, CA, United States) in default mode.
The peptide was identified by searching in the Swiss-Prot database using Protein Pilot TM 2.0 software (Applied Bio systems, Foster City, CA, United States) or Protein Prospector (http://prospector.ucsf.edu/). The ExPASy database (www.expasy.org/tools/pi_tool.html) was used to calculate the mono isotopic theoretical mass of the peptide.

Panayotov I.V., Végh A.G., Martin M., Vladimirov B., Larroque C., Gergely C., Cuisinier F.J, & Estephan E. (2023). Improving dental epithelial junction on dental implants with bioengineered peptides. Frontiers in Bioengineering and Biotechnology, 11, 1165853.

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Saliva Proteome Analysis in MCI and AD

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Saliva samples from four male subjects from each group (MCI, AD, and elderly nondemented controls) were pooled by mixing equal amounts. Fifty micrograms of each pool were loaded on a SDS-PAGE gel. ImageQuant software (GE Healthcare) was used for quantity determination.
Protein bands matching the corresponding molecular weight were excised from the gel and distained. In-gel digestion was carried out sequentially with trypsin and endopeptidase Asp-N for 16 h each. To validate the presence of lactoferrin in human saliva, this protein was identified by MALDI-TOF/TOF mass spectrometer 4800 Proteomics Analyzer (Applied Biosystems, Framingham, MA) and 4000 Series ExplorerTM software (Applied Biosystems).

Carro E., Bartolomé F., Bermejo-Pareja F., Villarejo-Galende A., Molina J.A., Ortiz P., Calero M., Rabano A., Cantero J.L, & Orive G. (2017). Early diagnosis of mild cognitive impairment and Alzheimer's disease based on salivary lactoferrin. Alzheimer's & Dementia : Diagnosis, Assessment & Disease Monitoring, 8, 131-138.

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MALDI-TOF/TOF Quantitative Analysis and Imaging

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A model 4800 MALDI TOF/TOF MS analyzer (Applied Biosystems, Framingham, MA, USA) equipped with a 200 Hz, 355 nm Nd:YAG laser was used for brain and PO extract quantitation and MALDI imaging. For sample spotting, 0.4 µL of sample was spotted on the stainless steel MALDI plate first, allowed to dry, and followed by the addition of 0.4 µL of matrix solution. The matrix used was 5 mg/mL of α-cyano-4-hydroxycinnamic acid (CHCA) in 50% acetonitrile (v/v). Each sample was spotted twice onto the MALDI plate, and one spectrum was obtained for each pair of spots. Acquisitions were performed in positive ion reflectron mode. Instrument parameters were set using the 4000 Series Explorer software (Applied Biosystems). Mass spectra were obtained by averaging 900 laser shots covering a mass range of m/z 500 to 4000.

Zhang Y., DeLaney K., Hui L., Wang J., Sturm R.M, & Li L. (2018). A Multifaceted Mass Spectrometric Method to Probe Feeding Related Neuropeptide Changes in Callinectes sapidus and Carcinus maenas. Journal of the American Society for Mass Spectrometry, 29(5), 948-960.

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MALDI-TOF-MS Profiling of Permethylated N-glycans

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Each permethylated N-glycan sample (0.5 μL) was spotted onto the MALDI plate, and 0.5 μL DHB (11 g/L in 50% methanol with 1 mmol/L sodium acetate) was added as a matrix solution. Each spot was then air-dried for 10 min. The data were generated with a MALDI-TOF-MS 4800 plus (Applied Biosystems) in positive reflector mode with the laser power set at 4880 and the digitizer set at 0.79. Each sample was run 3 times.
We selected 20 specific N-glycans for semiquantitative analysis and normalization of intensities to the sum of all the peaks. The ratios of the most abundant glycan (m/z 2792) and the internal standard (m/z 1357 or 926) were recorded to monitor the yield of glycan. We used 4000 series Explorer software (Applied Biosystems) to collect data and integrate peak intensities. All the glycans were identified as singly charged [M + Na]⁺.

Zhang W., James P.M., Ng B.G., Li X., Xia B., Rong J., Asif G., Raymond K., Jones M.A., Hegde M., Ju T., Cummings R.D., Clarkson K., Wood T., Boerkoel C.F., Freeze H.H, & He M. (2015). A Novel N-Tetrasaccharide in Patients with Congenital Disorders of Glycosylation Including Asparagine-Linked Glycosylation Protein 1, Phosphomannomutase 2, and Phosphomannose Isomerase Deficiencies. Clinical chemistry, 62(1), 208-217.

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Soluble Megalin Detection in Choroid Plexus

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Culture medium samples from choroid plexus epithelial cell culture were loaded on a SDS-PAGE 4–20% gel. A protein band matching the molecular weight of megalin was excised from the gel and destained. In-gel digestion was carried out sequentially with trypsin and endopeptidase Asp-N for 16 h each. To validate the presence of soluble megalin in culture medium, this protein was identified by a MALDI-TOF/TOF mass spectrometer 4800 Proteomics Analyzer (Applied Biosystems, Framingham, MA, USA) and 4000 Series Explorer™ software (Applied Biosystems).

Spuch C., Antequera D., Pascual C., Abilleira S., Blanco M., Moreno-Carretero M.J., Romero-López J., Ishida T., Molina J.A., Villarejo A., Bermejo-Pareja F, & Carro E. (2015). Soluble Megalin is Reduced in Cerebrospinal Fluid Samples of Alzheimer’s Disease Patients. Frontiers in Cellular Neuroscience, 9, 134.

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MALDI-TOF Mass Spectrometry Protocol

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Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry measurements were done using a 4800 MALDI-TOF/TOF Analyzer (Applied Biosystems). Mass spectra were recorded in the range from to 19,000 to 155,000 m/z in the linear positive ion mode. The data were recorded using 4000 Series Explorer Software and processed with Data Explorer Software version 4.9 (all from Applied Biosystems).

Streng-Ouwehand I., Ho N.I., Litjens M., Kalay H., Boks M.A., Cornelissen L.A., Kaur Singh S., Saeland E., Garcia-Vallejo J.J., Ossendorp F.A., Unger W.W, & van Kooyk Y. (2016). Glycan modification of antigen alters its intracellular routing in dendritic cells, promoting priming of T cells. eLife, 5, e11765.

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MALDI-TOF/TOF Protein Identification Protocol

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Samples were mixed with α-cyano-4-hydroxycinnamic acid 1∶5, v/v (5 mg/mL; Fluka, Switzerland) and spotted onto a metal plate. MS acquisition was performed with a 4800 Plus MALDI TOF/TOF analyzer (Applied Biosystems, Carlsbad, California, USA) equipped with a 200 Hz, 355 nm Nd:YAG laser. Ions were analyzed in reflectron mode using positive polarity. The instrument parameters were set using the 4000 Series Explorer software (version 3.5.3, Applied Biosystems). Mass spectra were obtained by averaging 1000 laser shots covering a mass range of m/z 900 to 4000. MS/MS of the 10 most intense precursor signals from MS spectra was achieved by 1 keV collision energy in positive ion mode with air as a collision gas and by averaging 1600 laser shots.
Data were analyzed using ProteinPilot (ProteinPilot^TM Software 4.5., 2012 AB SCIEX) [32] (link) for searching against the NCBI database using the Homo sapiens taxonomy. The search parameters allowed for two missed cleavage, trypsin digestion with a peptide tolerance = 0.3 Da and MS/MS tolerance = 0.5 Da. Only significant scores (greater than 39, p<0.05) for the peptides defined by a Mascot probability analysis were considered to be confidently identified peptides/proteins.

Sabol M., Trnski D., Uzarevic Z., Ozretic P., Musani V., Rafaj M., Cindric M, & Levanat S. (2014). Combination of Cyclopamine and Tamoxifen Promotes Survival and Migration of MCF-7 Breast Cancer Cells – Interaction of Hedgehog-Gli and Estrogen Receptor Signaling Pathways. PLoS ONE, 9(12), e114510.

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Protein Identification by MALDI-MS/MS Analysis

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2D-DIGE gels were silver stained to visualize the protein spots, and all differentially expressed protein spots were then manually excised and identified at the Hospital Nacional de Paraplejicos’ Proteomics Unit. The proteins were automatically digested in an “Ettan Digester” (GE Healthcare) according to Shevchenko et al. [13 (link)], with minor modifications. An aliquot of each digestion was mixed with an aliquot of the matrix solution and this mixture was pipetted directly onto the stainless steel sample plate of the mass spectrometer.
The MALDI-MS/MS data were obtained in an automated analysis loop using a 4800 Plus MALDI TOF/TOF Analyzer (Applied Biosystems). The spectra were acquired and the mass data were analysed automatically with the 4000 Series Explorer Software version 3.5.3 (Applied Biosystems). MALDI-MS and MS/MS data were combined through the GPS Explorer Software (Version 3.6) to search a non-redundant protein database (Swissprot 56.5) using the Mascot software (version 2.2: Matrix Science) [14 (link)].

Martin-Rojas T., Mourino-Alvarez L., Gil-Dones F., de la Cuesta F., Rosello-Lleti E., Laborde C.M., Rivera M., Lopez-Almodovar L.F., Lopez J.A., Akerstrom F., Padial L.R, & Barderas M.G. (2017). A clinical perspective on the utility of alpha 1 antichymotrypsin for the early diagnosis of calcific aortic stenosis. Clinical Proteomics, 14, 12.

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MALDI-TOF/TOF Mass Spectrometry Protocol

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MALDI-MS and MS/MS were carried out with a 4800 MALDI-TOF/TOF mass spectrometer (Applied Biosystems, Framingham, MA, USA). All mass spectra were obtained by averaging 2500 laser shots from each sample well in the positive-ion mode. For the MS/MS measurements, the metastable suppressor and CID gas were both set at “ON”. The entire process was controlled using 4000 series Explorer software (version 3.6; Applied Biosystems). Data were processed using Data Explorer software (version 4.8; Applied Biosystems). The MS/MS spectra were obtained with a fully automatic workflow using a 4800 MALDI-TOF/TOF analyzer. The resultant MS/MS spectra were processed using Mascot Distiller (Matrix Science Ltd, London, UK) and subjected to a database search by Mascot (MS/MS Ions Search).

Ieguchi K., Tomita T., Takao T., Omori T., Mishima T., Shimizu I., Tognolini M., Lodola A., Tsunoda T., Kobayashi S., Wada S, & Maru Y. (2021). Analysis of ADAM12-Mediated Ephrin-A1 Cleavage and Its Biological Functions. International Journal of Molecular Sciences, 22(5), 2480.

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MALDI-MS Protein Identification Protocol

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The MALDI MS spectra were converted into data with 4000 Series Explorer software (Applied Biosystems, Foster City, CA), and processed into a peptide mass fingerprint with Data Explorer software (Applied Biosystems, Foster City, CA). Protein identification using peptide mass fingerprints (PMF) from MALDI MS spectra were obtained using a GPS engine connected to a Mascot server provided by the software manufacturer. PMF were compared to known peptide mass sequences obtained from the NCBI database. Samples with a PMF with a high protein score (typically above 90%) were predicted to identify a particular protein.

Bend J.R., Xia X.Y., Chen D., Awaysheh A., Lo A., Rieder M.J, & Rylett R.J. (2015). Attenuation of Oxidative Stress in HEK 293 Cells by the TCM Constituents Schisanhenol, Baicalein, Resveratrol or Crocetin and Two Defined Mixtures. Journal of pharmacy & pharmaceutical sciences : a publication of the Canadian Society for Pharmaceutical Sciences, Societe canadienne des sciences pharmaceutiques, 18(4).

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