Role of Accurate Mass Measurement (±10 ppm) in Protein Identification Strategies Employing MS or MS/MS and Database Searching

Clauser, Karl R.; Baker, Peter R.; Burlingame, Alma L.

doi:10.1021/ac9810516

Cited by 1,068 publications

(838 citation statements)

References 63 publications

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“…80% sequence identity, although they added that these cases would need to be supported by further evidence for validation. The high mass accuracy of modern TOF and FT-MS instruments increases confidence in cross-species peptide mass mapping and loosen the sequence identity requirement, as less peptide masses would be required to produce a confident hit [10].…”

Section: Cross-species Protein Identification By Msmentioning

confidence: 99%

Expanding the organismal scope of proteomics: Cross‐species protein identification by mass spectrometry and its implications

2003

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Section: Cross-species Protein Identification By Msmentioning

confidence: 99%

Expanding the organismal scope of proteomics: Cross‐species protein identification by mass spectrometry and its implications

2003

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“…Very often, mass spectrometric data from tandem mass spectrometry (MS/MS) experiments using peptides from protein digests are employed [2][3][4]. One of the aspects of mass spectrometry, which is often viewed as the key to successful protein identification, is mass measurement accuracy (MMA) [5][6][7]. Increased mass accuracy allows the number of potential masses in a database to be reduced, and sufficiently high MMA may make a peptide unique within the context of a specific proteome [7].…”

mentioning

confidence: 99%

Mass measurement errors caused by “local” frequency perturbations in FTICR mass spectrometry

Masselon

Tolmachev

Anderson

et al. 2002

J. Am. Soc. Mass Spectrom.

102

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One of the key qualities of mass spectrometric measurements for biomolecules is the mass measurement accuracy (MMA) obtained. FTICR presently provides the highest MMA over a broad m/z range. However, due to space charge effects, the achievable MMA crucially depends on the number of ions trapped in the ICR cell for a measurement. Thus, beyond some point, as the effective sensitivity and dynamic range of a measurement increase, MMA tends to decrease. While analyzing deviations from the commonly used calibration law in FTICR we have found systematic errors which are not accounted for by a "global" space charge correction approach. The analysis of these errors and their dependence on charge population and post-excite radius have led us to conclude that each ion cloud experiences a different interaction with other ion clouds. We propose a novel calibration function which is shown to provide an improvement in MMA for all the spectra studied. (J Am Soc Mass Spectrom 2002, 13, 99 -106)

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“…Mass tolerance was 0.1 Da for identifying the fragment ions. The ProSight program was used to identify the c/z and b/y ion pairs whereas the a-type ions were identified from the Protein Prospector database [47]. Figure 1 shows a tandem mass spectrum of a nonphosphorylated reference peptide.…”

Section: Discussionmentioning

confidence: 99%

Identification of single and double sites of phosphorylation by ECD FT-ICR/MS in peptides related to the phosphorylation site domain of the myristoylated alanine-rich c kinase protein

Woodling

Eyler

Tsybin

et al. 2007

J. Am. Soc. Mass Spectrom.

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A series of phosphorylated test peptides was studied by electron capture dissociation Fourier transform ion cyclotron resonance mass spectrometry (ECD FT-ICR MS). The extensive ECD-induced fragmentation made identification of phosphorylation sites for these peptides straightforward. The site(s) of initial phosphorylation of a synthetic peptide with a sequence identical to that of the phosphorylation site domain (PSD) of the myristoylated alanine-rich C kinase (MARCKS) protein was then determined. Despite success in analyzing fragmentation of the smaller test peptides, a unique site on the PSD for the first step of phosphorylation could not be identified because the phosphorylation reaction produced a heterogeneous mixture of products. Some molecules were phosphorylated on the serine closest to the N-terminus, and others on one of the two serines closest to the C-terminus of the peptide. Although no definitive evidence for phosphorylation on either of the remaining two serines in the PSD was found, modification there could not be ruled out by the ECD fragmentation data. . This protein also binds calmodulin [7], acidic membrane phospholipids [8 -10], and actin filaments [11]. These interactions are believed to be regulated by protein phosphorylation [3,4,12,13]. The MARCKS protein is also a major substrate for protein kinase C (PKC) [14]. Protein kinase C-related kinase (PRK1) and -associated kinase also phosphorylate the phosphorylation site domain (PSD) [15,16]. PKC contains two regions: the N-terminal regulatory region and the C-terminal catalytic region. This kinase phosphorylates serine and threonine residues in basic peptide and protein sequences. Thus, PKC phosphorylates a small segment of the MARCKS protein, displacing the protein from membranes. The phosphorylation of the MARCKS protein then inhibits cross-linking activity of filamentous (F) actin, calcium-calmodulin binding, and binding to the plasma membrane [3,7,9,11,[17][18][19].The MARCKS protein contains three highly conserved regions: the phosphorylation site domain (PSD), the myristoylated amino-terminal domain, and the MARCKS homology domain. The PSD region, also known as the effector domain (ED), is the most studied, and is a basic peptide comprised of 25 amino acid residues. This region is believed to be central to the activity of the MARCKS protein.

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Role of Accurate Mass Measurement (±10 ppm) in Protein Identification Strategies Employing MS or MS/MS and Database Searching

Cited by 1,068 publications

References 63 publications

Expanding the organismal scope of proteomics: Cross‐species protein identification by mass spectrometry and its implications

Expanding the organismal scope of proteomics: Cross‐species protein identification by mass spectrometry and its implications

Mass measurement errors caused by “local” frequency perturbations in FTICR mass spectrometry

Identification of single and double sites of phosphorylation by ECD FT-ICR/MS in peptides related to the phosphorylation site domain of the myristoylated alanine-rich c kinase protein

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