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

MZ_CAMERA -- Error in FUN(X, Y, ...) : object 'res' not found

Jan, first of all, thank you for the extremely useful package.

I am experiencing problems when using the MZ_CAMERA function. I am not sure whether I am using it in the proper way, but I get this error:

Error in FUN(X, Y, ...) : object 'res' not found

This happens when I do this:

xsaFA <- findAdducts(xsaFI, polarity = "positive", rules = commonMZ::MZ_CAMERA(mode = "positive", warn_clash = T, clash_ppm = 30))

Also when I do this:

rules <- commonMZ::MZ_CAMERA(mode = "positive", warn_clash = T, clash_ppm = 30)

Any idea how to solve this issue?

I am using R 3.5.0 on an Ubuntu 18.04 machine.

My other question is about the usage of commonMZ alongside CAMERA. When is the appropriate time to run CAMERA with the rules provided in commonMZ? Should it be after the common CAMERA::annotate workflow? Does the following approach/order make any sense, for example?

xsa <- xsAnnotate(xset_conv, polarity = "positive", sample = c(1:dim(xset_conv@phenoData)[1]))
xsaF <- groupFWHM(xsa, perfwhm=0.6)
xsaC <- groupCorr(xsaF)
xsaFI <- findIsotopes(xsaC)
xsaFA <- findAdducts(xsaFI, polarity="positive")
xsaPL_default_CAMERA_rules <- getPeaklist(xsaFA)

positive_rule <- system.file('extdata/CAMERA_rules_pos.xlsx', package = "commonMZ")
positive_rule <- as.data.frame(readxl::read_xlsx(positive_rule))

xsaFA_contamin <- findAdducts(xsaFI, polarity = "positive", rules = positive_rule)
xsaPL_commonMZ <- getPeaklist(xsaFA_contamin)

Or is there a better approach to doing this?

stanstrup / commonmz Goto Github PK

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Add MS2Analyzer masses

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MZ_CAMERA -- Error in FUN(X, Y, ...) : object 'res' not found

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