Use of matrix clusters and trypsin autolysis fragments as mass calibrants in matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry

Harris, William A.; Janecki, Dariusz; Reilly, James P.

doi:10.1002/rcm.775

Cited by 65 publications

(60 citation statements)

References 19 publications

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“…Masses occurring in at least 5% of all PMFs were regarded as contaminants. In some cases peaks observed in less than 5% of the PMFs were also regarded as contaminants, because they had previously been described (␣-CHCA: 587.1, 641.1, 666.0, 699.2) [27] or were detected in a matrix reference spectrum. In total we elucidated 123 contaminant masses, which are listed in Table 1.…”

Section: Characteristics Of Peptide Masses: the Halfdecimal Place Rulementioning

confidence: 99%

Iterative data analysis is the key for exhaustive analysis of peptide mass fingerprints from proteins separated by two-dimensional electrophoresis

Schmidt

Schmid

Jungblut

et al. 2003

J. Am. Soc. Mass Spectrom.

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Peptide mass fingerprinting (PMF) is a powerful tool for identification of proteins separated by two-dimensional electrophoresis (2-DE). With the increase in sensitivity of peptide mass determination it becomes obvious that even spots looking well separated on a 2-DE gel may consist of several proteins. As a result the number of mass peaks in PMFs increased dramatically leaving many unassigned after a first database search. A number of these are caused by experiment-specific contaminants or by neighbor spots, as well as by additional proteins or post-translational modifications. To understand the complete protein composition of a spot we suggest an iterative procedure based on large numbers of PMFs, exemplified by PMFs of 480 Helicobacter pylori protein spots. Three key iterations were applied: (1) Elimination of contaminant mass peaks determined by MS-Screener (a software developed for this purpose) followed by reanalysis; (2) neighbor spot mass peak determination by cluster analysis, elimination from the peak list and repeated search; (3) re-evaluation of contaminant peaks. The quality of the identification was improved and spots previously unidentified were assigned to proteins. Eight additional spots were identified with this procedure, increasing the total number of identified spots to 455. [5][6][7], represent major milestones on the way to an understanding of the proteome. A further step was the application of mass spectrometry for peptide mass fingerprinting (PMF) instead of SDS gel electrophoresis [8], which resulted in a quick and reliable identification of 2-DE separated protein spots [9,10]. Instead of measuring the mass of the uncleaved proteins the high mass accuracy of MALDI-and ESI-MS in the Mr range between 500 and 3000 was utilized.PMF as a probability method is especially powerful if the data set of potential protein candidates is small, as in the case of microorganisms with completely sequenced genomes. For unequivocal identification of post-translational modifications, complementation by protein sequencing methods is necessary. PMF has been used successfully for the identification of several hundred proteins of Haemophilus influenzae [11], Mycobacterium tuberculosis [12], Helicobacter pylori [13], and Mycoplasma pneumoniae [14]. These investigations clearly demonstrated that proteins often occur as different protein species at different positions within the 2-DE gel. However, one spot may also represent several

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Section: Characteristics Of Peptide Masses: the Halfdecimal Place Rulementioning

confidence: 99%

Iterative data analysis is the key for exhaustive analysis of peptide mass fingerprints from proteins separated by two-dimensional electrophoresis

Schmidt

Schmid

Jungblut

et al. 2003

J. Am. Soc. Mass Spectrom.

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“…Precise calibration of ion masses is important to compare effects of different esterifications on shifting mass defect borders of native fragment ions (see Discussion), as well as to averaginescaling analysis. Use of ions in unoccupied spectral space for internal mass calibration is a previously explored concept [15].…”

Section: Internal Mass Calibration Using Iodine-containing Fragment Ionsmentioning

confidence: 99%

“…They have been used to introduce internal calibrants for mass spectrometry [15], to improve proteome profiling [5, 7, 9 -12], to analyze peptideoligonucleotide cross-links [16], and to determine protein post-translational modifications [17][18][19][20][21][22]. Due to the relatively large mass defects of oxygen and phosphorus atoms, phosphoryl fragment ions intersect with the unoccupied spectral space and are separated from most of isobaric native peptide fragment ions.…”

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confidence: 99%

Shifting unoccupied spectral space in mass spectrum of peptide fragment ions

Bajrami

Shi

Lapierre

et al. 2009

J. Am. Soc. Mass Spectrom.

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“…The fractional part of peptide masses can be predicted [19] and usually ranges from 0.4 to 0.7 Da for peptides between 1000 and 1100 Da [11]. This is a result of the contribution of near-integral masses of the elements typically found in peptides, such as C, H, N, O, and S [10,19]. This knowledge is useful for distinguishing peptides from molecules with a largely different elemental composition, such as those with large amounts of low-fractional mass elements such as the alkali metals, sodium, and potassium.…”

Section: Maldi Tof Mass Spectrometry Using Chcamentioning

confidence: 99%

“…Such a calculation may be useful in distinguishing these clusters from peptide signals. Nonetheless, these signals may complicate data analysis by increased spectral complexity but their value as internal mass calibrants in MALDI TOF mass spectrometry has been recognized [10]. Moreover, knowledge about matrix cluster masses may also be important when analyzing protein digests in order to exclude these signals from database searches for enhanced confidence scores [11].…”

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confidence: 99%

MALDI post-source decay and LIFT-TOF/TOF investigation of α-cyano-4-hydroxycinnamic acid cluster interferences

Neubert

Halket

Ocaña

et al. 2004

J. Am. Soc. Mass Spectrom.

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Large signals from ␣-cyano-4-hydroxycinnamic acid (CHCA) matrix complexes with sodium and potassium ions were found to interfere with sensitive matrix-assisted laser desorption/ ionization (MALDI) analysis of a hydrochloric acid digest of gelatine preparations. The nature of some selected matrix clusters was investigated by conventional post-source decay and LIFT-TOF/TOF experiments. The matrix clusters fragmented readily by neutral evaporation to give smaller sized matrix cluster species without matrix disintegration. Their characterization distinguished them from peptide signals, in particular from those that had the same nominal mass and differed only in the fractional part of the mass as encountered for gelatine-derived peptides. Knowledge of the molecular composition of these cluster species allowed using them for internal calibration of the MALDI mass spectra. The hydrolytic peptides could be analyzed with increased sensitivity when using 2,5-dihydroxy benzoic acid (DHB) as the MALDI matrix. (J Am Soc Mass Spectrom 2004, 15, 336 -343)

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Use of matrix clusters and trypsin autolysis fragments as mass calibrants in matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry

Cited by 65 publications

References 19 publications

Iterative data analysis is the key for exhaustive analysis of peptide mass fingerprints from proteins separated by two-dimensional electrophoresis

Iterative data analysis is the key for exhaustive analysis of peptide mass fingerprints from proteins separated by two-dimensional electrophoresis

Shifting unoccupied spectral space in mass spectrum of peptide fragment ions

MALDI post-source decay and LIFT-TOF/TOF investigation of α-cyano-4-hydroxycinnamic acid cluster interferences

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