README.md
In stanstrup/commonMZ: common_mz
commonMZ
This is a collection of common m/z values found in mass spectrometry.
The tables are available through an R package.
You can find the table files in the "inst\extdata" subfolder.
Contributions are welcomed.
It contains these tab delimited files:
contaminants_+.tsv: A table of common contaminant masses in positive ionization mode.
contaminants_-.tsv: A table of common contaminant masses in negative ionization mode.
adducts_fragments.tsv: A table of common fragment and adducts. The listed mass refers to mass differences.
repeating_units_+.tsv: A table of common series of repeated units (mass differences) in positive ionization mode.
* repeating_units_-.tsv: A table of common series of repeated units (mass differences) in negative ionization mode.
And these excel files:
CAMERA_rules_pos.xlsx: A table of common fragment and adducts for use with CAMERA in positive mode. The listed mass refers to mass differences to the uncharged species.
CAMERA_rules_neg.xlsx: A table of common fragment and adducts for use with CAMERA in negative mode. The listed mass refers to mass differences to the uncharged species.
* CAMERA_rules_EI.xlsx: A table of common fragment and adducts for use with CAMERA in EI mode. The listed mass refers to mass differences to the uncharged species.
Excel files are used to make it easier to work with since adducts/fragment types have been colored.
Glossary
| Type of ions: | Explanation |
|-------------------------|-----------------------------------------------------------------------|
| f+ | fragment ion |
| [f+H]+ | protonated fragment ion, e.g. in-source fragmentation of peptide ions |
| [M+H]+ | protonated molecular ion (pseudomolecular ion) |
| [M+Na]+ | sodiated molecular ion |
| [M+K]+ | potassiated molecular ion |
| [M2+H]+, [M3+H]+ etc... | protonated dimeric, trimeric, etc... molecular ion |
| [AnBm+H]+ | protonated moleuclar ion consisting of n A and m B subunits |
| Abbreviations | Explanation |
|---------------|-------------------------------------------------------------------------------|
| 4-HCCA | α-cyano-4-hydroxycinnamic acid, common matrix substance for MALDI MS analysis |
| 2,5-DHB | 2,5-Dihydroxy benzoic acid, common matrix substance for MALDI MS analysis |
| MeCN, ACN | acetonitrile, solvent |
| MeOH | methanol, solvent |
| MeNO2 | nitromethane, solvent |
| HABA | 2-(4-hydroxyphenyl-azo)-benzoic acid, matrix substance for MALDI MS analysis |
| SA | sinapic or sinapinic acid, common matrix substance for MALDI MS analysis |
| PEG | Polyethylene glycol, Repeat unit: -[O-CH2-CH2-]-; 44 Da |
| PPG | Polypropylene glycol, Repeat unit: -[O-C(CH3)H-CH2-]-; 58 Da |
| XaaCcamXaa | carbamidomethylated cysteine residue (+ICH2CONH2 - HI), +57Da |
| XaaMoxXaa | singly oxidized methionine residue (+O, 16 Da) |
References
The data in these tables are primarily from:
* the Supplementary Data from: Keller BO, Sui J, Young AB, Whittal RM. Interferences and contaminants encountered in modern mass spectrometry. Anal Chim Acta. 2008;627(1):71-81.
In the tables each entry references refers to the following table:
| Ref Label | Author(s) | Citation or Website/Download Information |
|-----------|---------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| A | Waters Corporation | Background Ion List online available at: www2.waters.com/CEConversion.nsf/files/3929E3EC20E43AAA8525710D004AB62E/$file/bkgrnd_ion_mstr_list.pdf |
| B | Applied Biosystems | Appendix D: Commonly Observed Background Ions: Mariner Biospectrometry's Workstation Users Guide |
| C | New Objective | Technical Note: Common Background Ions for Electrospray, online available at: http://www.newobjective.com/downloads/technotes/PV-3.pdf |
| D | Sigma-Aldrich | Chemical Formulas for Tween, Triton, and reduced Triton were adopted from the Sigma-Aldrich catalogue available online at: http://www.sigmaaldrich.com |
| E | Thermo Corporation, Mahn, B. | List of LC/MS contaminants online available at: www.abrf.org/index.cfm/list.msg/66994 |
| F | Tong, H.;Bell, D.; Tabei, K.; Siegel, M.M. | J. Am. Soc. Mass Spectrom., 10 (1999) 1174. |
| G | Andersen, J.S.; Kuester, B.; Podtelejnikov, A.; Mortz, E.; Mann, M. | Proc. 47th ASMS Conf. Mass Spectrom. Allied Topics, 1999, Dallas,TX, USA., |
| H | Keller, B.O.; Li, L. | J. Am. Soc. Mass Spectrom., 11 (2000) 88. |
| I | Keller, B.O.; Li, L.; Keller, H. | Program to predict and confirm matrix clusters masses, online available at: www.chem.ualberta.ca/~liweb/links/MaClust.htm |
| J | Harris,W.A.; Janecki, D.J.; Reilly, J.P. | Rapid Commun. Mass Spectrom., 16 (2002) 1714. |
| K | Keller, B.O.; Sui., J; Young, A.B.; Whittal, R.M.. | unpublished results; ESI background ions, Tween, Triton, PEGs, PPGs at www.chem.ualberta.ca/~massspec/es_ions.pdf (R.M. Whittal) |
| L | Schlosser, A.; Volkmer-Engert, R. | J. Mass Spectrom., 38 (2003) 523. |
| M | Tran, J.C.; Doucette, A.A. | J. Am. Soc. Mass Spectrom., 17 (2006) 652. |
| N | Verge, K.M.; Agnes, G.R. | J. Am. Soc. Mass Spectrom., 13 (2002) 901. |
| O | Paez, A.; Howe, A. | Canadian Chemical News, 56 (2004) 14. |
| P | Purves, R.W.; Gabryelski, W.; Li, L. | Rev. Sci. Instrument, 68 (1997) 3252. |
| Q | Gibson, C.R.; Brown, C.M. | J. Am. Soc. Mass spectrom., 14 (2003) 14. |
| R | Beavis,R. C.; Chait,B. T. | Anal. Chem., 62 (1990) 1836. |
| S | Guzzetta, A. | www.ionsource.com; Carbohydrate marker ions |
| T | Clauser, K.R.; Hall, S.C.; Smith, D.M.; Webb, J.W.; Andrews, L.E.; Tran, H.M.; Epstein, L.B; Burlingame, A.L. | Proc. Natl. Acad. Sci. U.S.A., 92 (1995) 5072., and http://prospector.ucsf.edu |
| U | Macha,S.F.; Limbach,P.A.; Hanton,S.D.; Owens,K.G. | J. Am. Soc. Mass Spectrom., 12 (2001), 732. |
| V | Pleasance,S.; Thibault,P.; Sim,P.G.; Boyd,R.K. | Rapid Commun. Mass Spectrom., 5 (1991) 307. |
| W | Xia,Y.-Q.; Patel,S.; Bakhtiar,R.; Franklin,R.B.; Doss,G.A. | J. Am. Soc. Mass Spectrom., 16 (2005) 417. |
| X | Guo,X.; Bruins,A.P.; Covey,T.R. | Rapid Commun. Mass Spectrom., 20 (2006) 3145. |
| Y | Ijames, C.F.; Dutky, R.C.; Fales, H.M. | J. Am. Soc. Mass Spectrom., 6 (1995) 1226. |
| Z | Hesse, M.; Meier, H.; Zeeh, B. | Spektroskopische Methoden in der organischen Chemie, Georg Thieme Verlag, Stuttgart, 3. Aufl. 1987, ISBN: 3-13-576103-7 |
| AA | Jan Stanstrup | None |
stanstrup/commonMZ documentation built on June 29, 2022, 12:01 p.m.
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commonMZ
This is a collection of common m/z values found in mass spectrometry. The tables are available through an R package. You can find the table files in the "inst\extdata" subfolder.
Contributions are welcomed.
It contains these tab delimited files:
contaminants_+.tsv: A table of common contaminant masses in positive ionization mode.
contaminants_-.tsv: A table of common contaminant masses in negative ionization mode.
adducts_fragments.tsv: A table of common fragment and adducts. The listed mass refers to mass differences.
repeating_units_+.tsv: A table of common series of repeated units (mass differences) in positive ionization mode.
* repeating_units_-.tsv: A table of common series of repeated units (mass differences) in negative ionization mode.
And these excel files:
CAMERA_rules_pos.xlsx: A table of common fragment and adducts for use with CAMERA in positive mode. The listed mass refers to mass differences to the uncharged species.
CAMERA_rules_neg.xlsx: A table of common fragment and adducts for use with CAMERA in negative mode. The listed mass refers to mass differences to the uncharged species.
* CAMERA_rules_EI.xlsx: A table of common fragment and adducts for use with CAMERA in EI mode. The listed mass refers to mass differences to the uncharged species.
Excel files are used to make it easier to work with since adducts/fragment types have been colored.
Glossary
| Type of ions: | Explanation | |-------------------------|-----------------------------------------------------------------------| | f+ | fragment ion | | [f+H]+ | protonated fragment ion, e.g. in-source fragmentation of peptide ions | | [M+H]+ | protonated molecular ion (pseudomolecular ion) | | [M+Na]+ | sodiated molecular ion | | [M+K]+ | potassiated molecular ion | | [M2+H]+, [M3+H]+ etc... | protonated dimeric, trimeric, etc... molecular ion | | [AnBm+H]+ | protonated moleuclar ion consisting of n A and m B subunits |
| Abbreviations | Explanation | |---------------|-------------------------------------------------------------------------------| | 4-HCCA | α-cyano-4-hydroxycinnamic acid, common matrix substance for MALDI MS analysis | | 2,5-DHB | 2,5-Dihydroxy benzoic acid, common matrix substance for MALDI MS analysis | | MeCN, ACN | acetonitrile, solvent | | MeOH | methanol, solvent | | MeNO2 | nitromethane, solvent | | HABA | 2-(4-hydroxyphenyl-azo)-benzoic acid, matrix substance for MALDI MS analysis | | SA | sinapic or sinapinic acid, common matrix substance for MALDI MS analysis | | PEG | Polyethylene glycol, Repeat unit: -[O-CH2-CH2-]-; 44 Da | | PPG | Polypropylene glycol, Repeat unit: -[O-C(CH3)H-CH2-]-; 58 Da | | XaaCcamXaa | carbamidomethylated cysteine residue (+ICH2CONH2 - HI), +57Da | | XaaMoxXaa | singly oxidized methionine residue (+O, 16 Da) |
References
The data in these tables are primarily from: * the Supplementary Data from: Keller BO, Sui J, Young AB, Whittal RM. Interferences and contaminants encountered in modern mass spectrometry. Anal Chim Acta. 2008;627(1):71-81.
In the tables each entry references refers to the following table:
| Ref Label | Author(s) | Citation or Website/Download Information | |-----------|---------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | A | Waters Corporation | Background Ion List online available at: www2.waters.com/CEConversion.nsf/files/3929E3EC20E43AAA8525710D004AB62E/$file/bkgrnd_ion_mstr_list.pdf | | B | Applied Biosystems | Appendix D: Commonly Observed Background Ions: Mariner Biospectrometry's Workstation Users Guide | | C | New Objective | Technical Note: Common Background Ions for Electrospray, online available at: http://www.newobjective.com/downloads/technotes/PV-3.pdf | | D | Sigma-Aldrich | Chemical Formulas for Tween, Triton, and reduced Triton were adopted from the Sigma-Aldrich catalogue available online at: http://www.sigmaaldrich.com | | E | Thermo Corporation, Mahn, B. | List of LC/MS contaminants online available at: www.abrf.org/index.cfm/list.msg/66994 | | F | Tong, H.;Bell, D.; Tabei, K.; Siegel, M.M. | J. Am. Soc. Mass Spectrom., 10 (1999) 1174. | | G | Andersen, J.S.; Kuester, B.; Podtelejnikov, A.; Mortz, E.; Mann, M. | Proc. 47th ASMS Conf. Mass Spectrom. Allied Topics, 1999, Dallas,TX, USA., | | H | Keller, B.O.; Li, L. | J. Am. Soc. Mass Spectrom., 11 (2000) 88. | | I | Keller, B.O.; Li, L.; Keller, H. | Program to predict and confirm matrix clusters masses, online available at: www.chem.ualberta.ca/~liweb/links/MaClust.htm | | J | Harris,W.A.; Janecki, D.J.; Reilly, J.P. | Rapid Commun. Mass Spectrom., 16 (2002) 1714. | | K | Keller, B.O.; Sui., J; Young, A.B.; Whittal, R.M.. | unpublished results; ESI background ions, Tween, Triton, PEGs, PPGs at www.chem.ualberta.ca/~massspec/es_ions.pdf (R.M. Whittal) | | L | Schlosser, A.; Volkmer-Engert, R. | J. Mass Spectrom., 38 (2003) 523. | | M | Tran, J.C.; Doucette, A.A. | J. Am. Soc. Mass Spectrom., 17 (2006) 652. | | N | Verge, K.M.; Agnes, G.R. | J. Am. Soc. Mass Spectrom., 13 (2002) 901. | | O | Paez, A.; Howe, A. | Canadian Chemical News, 56 (2004) 14. | | P | Purves, R.W.; Gabryelski, W.; Li, L. | Rev. Sci. Instrument, 68 (1997) 3252. | | Q | Gibson, C.R.; Brown, C.M. | J. Am. Soc. Mass spectrom., 14 (2003) 14. | | R | Beavis,R. C.; Chait,B. T. | Anal. Chem., 62 (1990) 1836. | | S | Guzzetta, A. | www.ionsource.com; Carbohydrate marker ions | | T | Clauser, K.R.; Hall, S.C.; Smith, D.M.; Webb, J.W.; Andrews, L.E.; Tran, H.M.; Epstein, L.B; Burlingame, A.L. | Proc. Natl. Acad. Sci. U.S.A., 92 (1995) 5072., and http://prospector.ucsf.edu | | U | Macha,S.F.; Limbach,P.A.; Hanton,S.D.; Owens,K.G. | J. Am. Soc. Mass Spectrom., 12 (2001), 732. | | V | Pleasance,S.; Thibault,P.; Sim,P.G.; Boyd,R.K. | Rapid Commun. Mass Spectrom., 5 (1991) 307. | | W | Xia,Y.-Q.; Patel,S.; Bakhtiar,R.; Franklin,R.B.; Doss,G.A. | J. Am. Soc. Mass Spectrom., 16 (2005) 417. | | X | Guo,X.; Bruins,A.P.; Covey,T.R. | Rapid Commun. Mass Spectrom., 20 (2006) 3145. | | Y | Ijames, C.F.; Dutky, R.C.; Fales, H.M. | J. Am. Soc. Mass Spectrom., 6 (1995) 1226. | | Z | Hesse, M.; Meier, H.; Zeeh, B. | Spektroskopische Methoden in der organischen Chemie, Georg Thieme Verlag, Stuttgart, 3. Aufl. 1987, ISBN: 3-13-576103-7 | | AA | Jan Stanstrup | None |
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