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A collection of common mz values found in mass spectrometry.

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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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