ion trap Search Results


ion trap mass spectrometer  (SIMAC Electronics)
90
SIMAC Electronics ion trap mass spectrometer
The work flow for proteomic and bioinformatics PTM analysis is illustrated . [A] Proteins isolated from kinase assays are in-solution digested into peptides using the proteases Lysyl Endopeptidase and Trypsin. The peptides containing specific post-translational modifications (phosphorylation) are enriched using different resins. Non-modified peptides are used to identify proteins. [B] Purified peptides are separated on a miniaturized reverse phase chromatography column with an organic solvent gradient. Peptides eluting from the column are ionized by electrospray at the tip of the column, directly in front of the mass <t>spectrometer.</t> [C] The electrosprayed ions are transferred into the vacuum of the mass spectrometer. In the mass spectrometer (MS mode) all ions are moved to the mass analyzer (ion Trap), where they are measured at high resolution. The mass analyser then selects a particular peptide ion and fragments it in a collision cell. For modified peptides, the peptide mass will be shifted by the mass of the modification, as will all fragments containing the modification, allowing the unambiguous placement of the PTM on the sequence. [D] The mass and lists of fragment masses for each peptide are scanned against protein sequence databases, resulting in a list of identified peptides and proteins. The lists of proteins and their peptides are the basis for bioinformatics analysis, in order to acknowledge improvements.
Ion Trap Mass Spectrometer, supplied by SIMAC Electronics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/ion+trap/ion+trap+mass+spectrometer/pmc03164609-41-27-23
Average 90 stars, based on 1 article reviews
ion trap mass spectrometer - by Bioz Stars, 2026-09
90/100 stars
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ion trap  (FormFactor Inc)
90
FormFactor Inc ion trap
The work flow for proteomic and bioinformatics PTM analysis is illustrated . [A] Proteins isolated from kinase assays are in-solution digested into peptides using the proteases Lysyl Endopeptidase and Trypsin. The peptides containing specific post-translational modifications (phosphorylation) are enriched using different resins. Non-modified peptides are used to identify proteins. [B] Purified peptides are separated on a miniaturized reverse phase chromatography column with an organic solvent gradient. Peptides eluting from the column are ionized by electrospray at the tip of the column, directly in front of the mass <t>spectrometer.</t> [C] The electrosprayed ions are transferred into the vacuum of the mass spectrometer. In the mass spectrometer (MS mode) all ions are moved to the mass analyzer (ion Trap), where they are measured at high resolution. The mass analyser then selects a particular peptide ion and fragments it in a collision cell. For modified peptides, the peptide mass will be shifted by the mass of the modification, as will all fragments containing the modification, allowing the unambiguous placement of the PTM on the sequence. [D] The mass and lists of fragment masses for each peptide are scanned against protein sequence databases, resulting in a list of identified peptides and proteins. The lists of proteins and their peptides are the basis for bioinformatics analysis, in order to acknowledge improvements.
Ion Trap, supplied by FormFactor Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/ion+trap/ion+trap/10__1364_slash_oe__531050-27-13-8
Average 90 stars, based on 1 article reviews
ion trap - by Bioz Stars, 2026-09
90/100 stars
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quadrupole ion trap mass spectrometer  (COMPAS Inc)
90
COMPAS Inc quadrupole ion trap mass spectrometer
The work flow for proteomic and bioinformatics PTM analysis is illustrated . [A] Proteins isolated from kinase assays are in-solution digested into peptides using the proteases Lysyl Endopeptidase and Trypsin. The peptides containing specific post-translational modifications (phosphorylation) are enriched using different resins. Non-modified peptides are used to identify proteins. [B] Purified peptides are separated on a miniaturized reverse phase chromatography column with an organic solvent gradient. Peptides eluting from the column are ionized by electrospray at the tip of the column, directly in front of the mass <t>spectrometer.</t> [C] The electrosprayed ions are transferred into the vacuum of the mass spectrometer. In the mass spectrometer (MS mode) all ions are moved to the mass analyzer (ion Trap), where they are measured at high resolution. The mass analyser then selects a particular peptide ion and fragments it in a collision cell. For modified peptides, the peptide mass will be shifted by the mass of the modification, as will all fragments containing the modification, allowing the unambiguous placement of the PTM on the sequence. [D] The mass and lists of fragment masses for each peptide are scanned against protein sequence databases, resulting in a list of identified peptides and proteins. The lists of proteins and their peptides are the basis for bioinformatics analysis, in order to acknowledge improvements.
Quadrupole Ion Trap Mass Spectrometer, supplied by COMPAS Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/ion+trap/quadrupole+ion+trap+mass+spectrometer/pm15047056-3-31-9
Average 90 stars, based on 1 article reviews
quadrupole ion trap mass spectrometer - by Bioz Stars, 2026-09
90/100 stars
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livermore electron beam ion traps ebit-i and ebit-ii  (Lawrence Livermore National Security LLC)
90
Lawrence Livermore National Security LLC livermore electron beam ion traps ebit-i and ebit-ii
The work flow for proteomic and bioinformatics PTM analysis is illustrated . [A] Proteins isolated from kinase assays are in-solution digested into peptides using the proteases Lysyl Endopeptidase and Trypsin. The peptides containing specific post-translational modifications (phosphorylation) are enriched using different resins. Non-modified peptides are used to identify proteins. [B] Purified peptides are separated on a miniaturized reverse phase chromatography column with an organic solvent gradient. Peptides eluting from the column are ionized by electrospray at the tip of the column, directly in front of the mass <t>spectrometer.</t> [C] The electrosprayed ions are transferred into the vacuum of the mass spectrometer. In the mass spectrometer (MS mode) all ions are moved to the mass analyzer (ion Trap), where they are measured at high resolution. The mass analyser then selects a particular peptide ion and fragments it in a collision cell. For modified peptides, the peptide mass will be shifted by the mass of the modification, as will all fragments containing the modification, allowing the unambiguous placement of the PTM on the sequence. [D] The mass and lists of fragment masses for each peptide are scanned against protein sequence databases, resulting in a list of identified peptides and proteins. The lists of proteins and their peptides are the basis for bioinformatics analysis, in order to acknowledge improvements.
Livermore Electron Beam Ion Traps Ebit I And Ebit Ii, supplied by Lawrence Livermore National Security LLC, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/ion+trap/ebit+ii+electron+beam+ion+trap/10__1103_slash_physreve__84__046402-6-7-29
Average 90 stars, based on 1 article reviews
livermore electron beam ion traps ebit-i and ebit-ii - by Bioz Stars, 2026-09
90/100 stars
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human ion trap spectral library  (National Institute of Standards and Technology)
90
National Institute of Standards and Technology human ion trap spectral library
The work flow for proteomic and bioinformatics PTM analysis is illustrated . [A] Proteins isolated from kinase assays are in-solution digested into peptides using the proteases Lysyl Endopeptidase and Trypsin. The peptides containing specific post-translational modifications (phosphorylation) are enriched using different resins. Non-modified peptides are used to identify proteins. [B] Purified peptides are separated on a miniaturized reverse phase chromatography column with an organic solvent gradient. Peptides eluting from the column are ionized by electrospray at the tip of the column, directly in front of the mass <t>spectrometer.</t> [C] The electrosprayed ions are transferred into the vacuum of the mass spectrometer. In the mass spectrometer (MS mode) all ions are moved to the mass analyzer (ion Trap), where they are measured at high resolution. The mass analyser then selects a particular peptide ion and fragments it in a collision cell. For modified peptides, the peptide mass will be shifted by the mass of the modification, as will all fragments containing the modification, allowing the unambiguous placement of the PTM on the sequence. [D] The mass and lists of fragment masses for each peptide are scanned against protein sequence databases, resulting in a list of identified peptides and proteins. The lists of proteins and their peptides are the basis for bioinformatics analysis, in order to acknowledge improvements.
Human Ion Trap Spectral Library, supplied by National Institute of Standards and Technology, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/ion+trap/human+ion+trap+spectral+library/pmc03606982-248-12-7
Average 90 stars, based on 1 article reviews
human ion trap spectral library - by Bioz Stars, 2026-09
90/100 stars
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hybrid tandem mass spectrometer with a linear ion trap  (Verlag GmbH)
90
Verlag GmbH hybrid tandem mass spectrometer with a linear ion trap
The work flow for proteomic and bioinformatics PTM analysis is illustrated . [A] Proteins isolated from kinase assays are in-solution digested into peptides using the proteases Lysyl Endopeptidase and Trypsin. The peptides containing specific post-translational modifications (phosphorylation) are enriched using different resins. Non-modified peptides are used to identify proteins. [B] Purified peptides are separated on a miniaturized reverse phase chromatography column with an organic solvent gradient. Peptides eluting from the column are ionized by electrospray at the tip of the column, directly in front of the mass <t>spectrometer.</t> [C] The electrosprayed ions are transferred into the vacuum of the mass spectrometer. In the mass spectrometer (MS mode) all ions are moved to the mass analyzer (ion Trap), where they are measured at high resolution. The mass analyser then selects a particular peptide ion and fragments it in a collision cell. For modified peptides, the peptide mass will be shifted by the mass of the modification, as will all fragments containing the modification, allowing the unambiguous placement of the PTM on the sequence. [D] The mass and lists of fragment masses for each peptide are scanned against protein sequence databases, resulting in a list of identified peptides and proteins. The lists of proteins and their peptides are the basis for bioinformatics analysis, in order to acknowledge improvements.
Hybrid Tandem Mass Spectrometer With A Linear Ion Trap, supplied by Verlag GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/ion+trap/hybrid+tandem+mass+spectrometer+with+a+linear+ion+trap/pm20107771-11-29-6
Average 90 stars, based on 1 article reviews
hybrid tandem mass spectrometer with a linear ion trap - by Bioz Stars, 2026-09
90/100 stars
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ion trap ms/ms  (Verlag GmbH)
90
Verlag GmbH ion trap ms/ms
The work flow for proteomic and bioinformatics PTM analysis is illustrated . [A] Proteins isolated from kinase assays are in-solution digested into peptides using the proteases Lysyl Endopeptidase and Trypsin. The peptides containing specific post-translational modifications (phosphorylation) are enriched using different resins. Non-modified peptides are used to identify proteins. [B] Purified peptides are separated on a miniaturized reverse phase chromatography column with an organic solvent gradient. Peptides eluting from the column are ionized by electrospray at the tip of the column, directly in front of the mass <t>spectrometer.</t> [C] The electrosprayed ions are transferred into the vacuum of the mass spectrometer. In the mass spectrometer (MS mode) all ions are moved to the mass analyzer (ion Trap), where they are measured at high resolution. The mass analyser then selects a particular peptide ion and fragments it in a collision cell. For modified peptides, the peptide mass will be shifted by the mass of the modification, as will all fragments containing the modification, allowing the unambiguous placement of the PTM on the sequence. [D] The mass and lists of fragment masses for each peptide are scanned against protein sequence databases, resulting in a list of identified peptides and proteins. The lists of proteins and their peptides are the basis for bioinformatics analysis, in order to acknowledge improvements.
Ion Trap Ms/Ms, supplied by Verlag GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/ion+trap/ion+trap/pm19953542-103-11-3
Average 90 stars, based on 1 article reviews
ion trap ms/ms - by Bioz Stars, 2026-09
90/100 stars
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quadrupole ion trap  (Jordan TOF Products Inc)
90
Jordan TOF Products Inc quadrupole ion trap
The work flow for proteomic and bioinformatics PTM analysis is illustrated . [A] Proteins isolated from kinase assays are in-solution digested into peptides using the proteases Lysyl Endopeptidase and Trypsin. The peptides containing specific post-translational modifications (phosphorylation) are enriched using different resins. Non-modified peptides are used to identify proteins. [B] Purified peptides are separated on a miniaturized reverse phase chromatography column with an organic solvent gradient. Peptides eluting from the column are ionized by electrospray at the tip of the column, directly in front of the mass <t>spectrometer.</t> [C] The electrosprayed ions are transferred into the vacuum of the mass spectrometer. In the mass spectrometer (MS mode) all ions are moved to the mass analyzer (ion Trap), where they are measured at high resolution. The mass analyser then selects a particular peptide ion and fragments it in a collision cell. For modified peptides, the peptide mass will be shifted by the mass of the modification, as will all fragments containing the modification, allowing the unambiguous placement of the PTM on the sequence. [D] The mass and lists of fragment masses for each peptide are scanned against protein sequence databases, resulting in a list of identified peptides and proteins. The lists of proteins and their peptides are the basis for bioinformatics analysis, in order to acknowledge improvements.
Quadrupole Ion Trap, supplied by Jordan TOF Products Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/ion+trap/quadrupole+ion+trap/ppr0391939-77-17-20
Average 90 stars, based on 1 article reviews
quadrupole ion trap - by Bioz Stars, 2026-09
90/100 stars
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electron-beam ion trap ebit  (Lawrence Livermore National Security LLC)
90
Lawrence Livermore National Security LLC electron-beam ion trap ebit
The work flow for proteomic and bioinformatics PTM analysis is illustrated . [A] Proteins isolated from kinase assays are in-solution digested into peptides using the proteases Lysyl Endopeptidase and Trypsin. The peptides containing specific post-translational modifications (phosphorylation) are enriched using different resins. Non-modified peptides are used to identify proteins. [B] Purified peptides are separated on a miniaturized reverse phase chromatography column with an organic solvent gradient. Peptides eluting from the column are ionized by electrospray at the tip of the column, directly in front of the mass <t>spectrometer.</t> [C] The electrosprayed ions are transferred into the vacuum of the mass spectrometer. In the mass spectrometer (MS mode) all ions are moved to the mass analyzer (ion Trap), where they are measured at high resolution. The mass analyser then selects a particular peptide ion and fragments it in a collision cell. For modified peptides, the peptide mass will be shifted by the mass of the modification, as will all fragments containing the modification, allowing the unambiguous placement of the PTM on the sequence. [D] The mass and lists of fragment masses for each peptide are scanned against protein sequence databases, resulting in a list of identified peptides and proteins. The lists of proteins and their peptides are the basis for bioinformatics analysis, in order to acknowledge improvements.
Electron Beam Ion Trap Ebit, supplied by Lawrence Livermore National Security LLC, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/ion+trap/electron+beam+ion+trap+ebit/10__1103_slash_physreva__109__063108-24-26-20
Average 90 stars, based on 1 article reviews
electron-beam ion trap ebit - by Bioz Stars, 2026-09
90/100 stars
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electron beam ion trap (ebit)  (Lawrence Livermore National Security LLC)
90
Lawrence Livermore National Security LLC electron beam ion trap (ebit)
The work flow for proteomic and bioinformatics PTM analysis is illustrated . [A] Proteins isolated from kinase assays are in-solution digested into peptides using the proteases Lysyl Endopeptidase and Trypsin. The peptides containing specific post-translational modifications (phosphorylation) are enriched using different resins. Non-modified peptides are used to identify proteins. [B] Purified peptides are separated on a miniaturized reverse phase chromatography column with an organic solvent gradient. Peptides eluting from the column are ionized by electrospray at the tip of the column, directly in front of the mass <t>spectrometer.</t> [C] The electrosprayed ions are transferred into the vacuum of the mass spectrometer. In the mass spectrometer (MS mode) all ions are moved to the mass analyzer (ion Trap), where they are measured at high resolution. The mass analyser then selects a particular peptide ion and fragments it in a collision cell. For modified peptides, the peptide mass will be shifted by the mass of the modification, as will all fragments containing the modification, allowing the unambiguous placement of the PTM on the sequence. [D] The mass and lists of fragment masses for each peptide are scanned against protein sequence databases, resulting in a list of identified peptides and proteins. The lists of proteins and their peptides are the basis for bioinformatics analysis, in order to acknowledge improvements.
Electron Beam Ion Trap (Ebit), supplied by Lawrence Livermore National Security LLC, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/ion+trap/electron+beam+ion+trap/10__3390_slash_atoms3030367-22-33-6
Average 90 stars, based on 1 article reviews
electron beam ion trap (ebit) - by Bioz Stars, 2026-09
90/100 stars
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superebit electron beam ion trap (ebit) facility  (Lawrence Livermore National Security LLC)
90
Lawrence Livermore National Security LLC superebit electron beam ion trap (ebit) facility
The work flow for proteomic and bioinformatics PTM analysis is illustrated . [A] Proteins isolated from kinase assays are in-solution digested into peptides using the proteases Lysyl Endopeptidase and Trypsin. The peptides containing specific post-translational modifications (phosphorylation) are enriched using different resins. Non-modified peptides are used to identify proteins. [B] Purified peptides are separated on a miniaturized reverse phase chromatography column with an organic solvent gradient. Peptides eluting from the column are ionized by electrospray at the tip of the column, directly in front of the mass <t>spectrometer.</t> [C] The electrosprayed ions are transferred into the vacuum of the mass spectrometer. In the mass spectrometer (MS mode) all ions are moved to the mass analyzer (ion Trap), where they are measured at high resolution. The mass analyser then selects a particular peptide ion and fragments it in a collision cell. For modified peptides, the peptide mass will be shifted by the mass of the modification, as will all fragments containing the modification, allowing the unambiguous placement of the PTM on the sequence. [D] The mass and lists of fragment masses for each peptide are scanned against protein sequence databases, resulting in a list of identified peptides and proteins. The lists of proteins and their peptides are the basis for bioinformatics analysis, in order to acknowledge improvements.
Superebit Electron Beam Ion Trap (Ebit) Facility, supplied by Lawrence Livermore National Security LLC, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/ion+trap/superebit+electron+beam+ion+trap/10__1088_slash_1742___6596_slash_163_slash_1_slash_012052-10-47-55
Average 90 stars, based on 1 article reviews
superebit electron beam ion trap (ebit) facility - by Bioz Stars, 2026-09
90/100 stars
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3200 q trap® lc-ms/ms system  (Weinmann GmbH)
90
Weinmann GmbH 3200 q trap® lc-ms/ms system
The work flow for proteomic and bioinformatics PTM analysis is illustrated . [A] Proteins isolated from kinase assays are in-solution digested into peptides using the proteases Lysyl Endopeptidase and Trypsin. The peptides containing specific post-translational modifications (phosphorylation) are enriched using different resins. Non-modified peptides are used to identify proteins. [B] Purified peptides are separated on a miniaturized reverse phase chromatography column with an organic solvent gradient. Peptides eluting from the column are ionized by electrospray at the tip of the column, directly in front of the mass <t>spectrometer.</t> [C] The electrosprayed ions are transferred into the vacuum of the mass spectrometer. In the mass spectrometer (MS mode) all ions are moved to the mass analyzer (ion Trap), where they are measured at high resolution. The mass analyser then selects a particular peptide ion and fragments it in a collision cell. For modified peptides, the peptide mass will be shifted by the mass of the modification, as will all fragments containing the modification, allowing the unambiguous placement of the PTM on the sequence. [D] The mass and lists of fragment masses for each peptide are scanned against protein sequence databases, resulting in a list of identified peptides and proteins. The lists of proteins and their peptides are the basis for bioinformatics analysis, in order to acknowledge improvements.
3200 Q Trap® Lc Ms/Ms System, supplied by Weinmann GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/ion+trap/ion+trap+mass+spectrometer/10__1007_slash_978___1___4939___7899___1-5338-22-8
Average 90 stars, based on 1 article reviews
3200 q trap® lc-ms/ms system - by Bioz Stars, 2026-09
90/100 stars
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Image Search Results


The work flow for proteomic and bioinformatics PTM analysis is illustrated . [A] Proteins isolated from kinase assays are in-solution digested into peptides using the proteases Lysyl Endopeptidase and Trypsin. The peptides containing specific post-translational modifications (phosphorylation) are enriched using different resins. Non-modified peptides are used to identify proteins. [B] Purified peptides are separated on a miniaturized reverse phase chromatography column with an organic solvent gradient. Peptides eluting from the column are ionized by electrospray at the tip of the column, directly in front of the mass spectrometer. [C] The electrosprayed ions are transferred into the vacuum of the mass spectrometer. In the mass spectrometer (MS mode) all ions are moved to the mass analyzer (ion Trap), where they are measured at high resolution. The mass analyser then selects a particular peptide ion and fragments it in a collision cell. For modified peptides, the peptide mass will be shifted by the mass of the modification, as will all fragments containing the modification, allowing the unambiguous placement of the PTM on the sequence. [D] The mass and lists of fragment masses for each peptide are scanned against protein sequence databases, resulting in a list of identified peptides and proteins. The lists of proteins and their peptides are the basis for bioinformatics analysis, in order to acknowledge improvements.

Journal: Journal of Clinical Bioinformatics

Article Title: Discovering and validating unknown phospho-sites from p38 and HuR protein kinases in vitro by Phosphoproteomic and Bioinformatic tools

doi: 10.1186/2043-9113-1-16

Figure Lengend Snippet: The work flow for proteomic and bioinformatics PTM analysis is illustrated . [A] Proteins isolated from kinase assays are in-solution digested into peptides using the proteases Lysyl Endopeptidase and Trypsin. The peptides containing specific post-translational modifications (phosphorylation) are enriched using different resins. Non-modified peptides are used to identify proteins. [B] Purified peptides are separated on a miniaturized reverse phase chromatography column with an organic solvent gradient. Peptides eluting from the column are ionized by electrospray at the tip of the column, directly in front of the mass spectrometer. [C] The electrosprayed ions are transferred into the vacuum of the mass spectrometer. In the mass spectrometer (MS mode) all ions are moved to the mass analyzer (ion Trap), where they are measured at high resolution. The mass analyser then selects a particular peptide ion and fragments it in a collision cell. For modified peptides, the peptide mass will be shifted by the mass of the modification, as will all fragments containing the modification, allowing the unambiguous placement of the PTM on the sequence. [D] The mass and lists of fragment masses for each peptide are scanned against protein sequence databases, resulting in a list of identified peptides and proteins. The lists of proteins and their peptides are the basis for bioinformatics analysis, in order to acknowledge improvements.

Article Snippet: In this study, MSA (multistage activation) compared to DDNLMS3 (neutral loss MS3) gave more information for the suite of phosphopeptides studied when using SIMAC coupled to the ion Trap mass spectrometer.

Techniques: Isolation, Phospho-proteomics, Modification, Purification, Reversed-phase Chromatography, Solvent, Mass Spectrometry, Sequencing

The 3 phosphorylated proteins (HuR, Chain B and p38p) and the 6 phosphopeptides identified and validated (amino acid sequences below the identified proteins) when using SIMAC coupled to MAS by the LTQ ion Trap mass spectrometer are shown in this table.

Journal: Journal of Clinical Bioinformatics

Article Title: Discovering and validating unknown phospho-sites from p38 and HuR protein kinases in vitro by Phosphoproteomic and Bioinformatic tools

doi: 10.1186/2043-9113-1-16

Figure Lengend Snippet: The 3 phosphorylated proteins (HuR, Chain B and p38p) and the 6 phosphopeptides identified and validated (amino acid sequences below the identified proteins) when using SIMAC coupled to MAS by the LTQ ion Trap mass spectrometer are shown in this table.

Article Snippet: In this study, MSA (multistage activation) compared to DDNLMS3 (neutral loss MS3) gave more information for the suite of phosphopeptides studied when using SIMAC coupled to the ion Trap mass spectrometer.

Techniques: Mass Spectrometry, RNA Binding Assay, Ubiquitin Proteomics, Activation Assay

The efficiency and reproducibility of the phosphopeptide purification and identification when using ~3 μg of protein kinases per each resin and/or phosphoenrichment method (SIMAC, TiO 2 and IMAC) coupled to R3/C18 and MSA-LTQ ion Trap mass spectrometer is illustrated . [A] Four triplicate experiments were carried out in order to identify the phosphopeptides. The phospho-site identifications were carried out from pooled and non-pooled assays (inter- and intra-assays) confirming a high reproducibility. The 6 phosphorylated peptides identified were isolated and validated in the four triplicate analyses, not only by Mascot (at least 4 continuously -y and -b ions matched)but also by manual inspection of all the spectra. SIMAC allowed the purification of 3 phosphorylated proteins: HuR RNA binding, p38 MAP Kinase and Trapped Ubiquitin-Like Protein Activation Complex, and 6 phosphorylated peptides related to those previously mentioned proteins. TiO 2 and IMAC allowed the isolation of 2 phoshorylated proteins: HuR RNA binding and p38 MAP Kinase, and 1 phosphopeptide related to the protein kinase HuR RNA binding. [B] SIMAC coupled to MSA allowed the identification of one more phosphopeptide compared to SIMAC coupled to DDNLMS3. Nevertheless, both strategies (SIMAC coupled to MSA and SIMAC coupled to DDNLMS3) allowed the identification of the same number of phosphorylated proteins (3). [C] and [D] Three phosphorylated proteins and six phosphopeptides were identified when using SIMAC coupled to MSA. From those three phosphoproteins identified, six phosphopeptides were identified: (a) TiO 2 coupled to MSA allowed the identification of two equal/same phosphorylated proteins and four equal/same phosphopeptides as SIMAC and (b) IMAC allowed the identification of one equal/same protein and two equal/same phosphopeptides. Thus, SIMAC is more efficient than the other tested resins for this study, while TiO 2 and IMAC corroborate the reproducibility of the phosphorylated proteins and phosphopeptides identified.

Journal: Journal of Clinical Bioinformatics

Article Title: Discovering and validating unknown phospho-sites from p38 and HuR protein kinases in vitro by Phosphoproteomic and Bioinformatic tools

doi: 10.1186/2043-9113-1-16

Figure Lengend Snippet: The efficiency and reproducibility of the phosphopeptide purification and identification when using ~3 μg of protein kinases per each resin and/or phosphoenrichment method (SIMAC, TiO 2 and IMAC) coupled to R3/C18 and MSA-LTQ ion Trap mass spectrometer is illustrated . [A] Four triplicate experiments were carried out in order to identify the phosphopeptides. The phospho-site identifications were carried out from pooled and non-pooled assays (inter- and intra-assays) confirming a high reproducibility. The 6 phosphorylated peptides identified were isolated and validated in the four triplicate analyses, not only by Mascot (at least 4 continuously -y and -b ions matched)but also by manual inspection of all the spectra. SIMAC allowed the purification of 3 phosphorylated proteins: HuR RNA binding, p38 MAP Kinase and Trapped Ubiquitin-Like Protein Activation Complex, and 6 phosphorylated peptides related to those previously mentioned proteins. TiO 2 and IMAC allowed the isolation of 2 phoshorylated proteins: HuR RNA binding and p38 MAP Kinase, and 1 phosphopeptide related to the protein kinase HuR RNA binding. [B] SIMAC coupled to MSA allowed the identification of one more phosphopeptide compared to SIMAC coupled to DDNLMS3. Nevertheless, both strategies (SIMAC coupled to MSA and SIMAC coupled to DDNLMS3) allowed the identification of the same number of phosphorylated proteins (3). [C] and [D] Three phosphorylated proteins and six phosphopeptides were identified when using SIMAC coupled to MSA. From those three phosphoproteins identified, six phosphopeptides were identified: (a) TiO 2 coupled to MSA allowed the identification of two equal/same phosphorylated proteins and four equal/same phosphopeptides as SIMAC and (b) IMAC allowed the identification of one equal/same protein and two equal/same phosphopeptides. Thus, SIMAC is more efficient than the other tested resins for this study, while TiO 2 and IMAC corroborate the reproducibility of the phosphorylated proteins and phosphopeptides identified.

Article Snippet: In this study, MSA (multistage activation) compared to DDNLMS3 (neutral loss MS3) gave more information for the suite of phosphopeptides studied when using SIMAC coupled to the ion Trap mass spectrometer.

Techniques: Phospho-proteomics, Purification, Mass Spectrometry, Isolation, RNA Binding Assay, Ubiquitin Proteomics, Activation Assay