Supplementary Information. Ionization Mass Spectrometry

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1 Supplementary Information Rapid Discrimination of Bacteria by Paper Spray Ionization Mass Spectrometry Ahmed M. Hamid a, Alan K. Jarmusch a, Valentina Pirro b, David H. Pincus c, Bradford G. Clay c, Gaspard Gervasi d, and R. Graham Cooks a * a Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University, West Lafayette, IN 4797 b Department of Chemistry, University of Turin, Turin, Italy c biomérieux, Inc., Hazelwood, MO 6342 d biomérieux, Marcy l Etoile, France KEYWORDS: Bacterial discrimination, ambient ionization, phospholipids, chemometrics, multivariate statistics, tandem mass spectrometry, data fusion 1

2 ABSTRACT: Paper spray mass spectrometry ionization is utilized for rapid discrimination of bacteria without sample preparation. Bacterial colonies were smeared onto filter paper pre-cut to a sharp point, then wetted with solvent and held at a high potential. Charged droplets released by field emission were sucked into the mass spectrometer inlet and mass spectra were recorded. Sixteen different species representing eight different genera from gram-positive and gramnegative bacteria were investigated. Phospholipids were the predominant species observed in the mass-spectra in both the negative and positive ion modes. Multivariate data analysis based on principal component analysis, followed by linear discriminant analysis, allowed bacterial discrimination. The lipid information in the negative ion mass spectra proved useful for specieslevel differentiation of the investigated gram-positive bacteria. Gram-negative bacteria were differentiated at the species-level by using a numerical data fusion strategy of positive and negative ion mass spectra. Supplementary Methods Chemicals and Materials Methanol (HPLC grade) was purchased from Mallinckrodt Baker Inc. (Phillipsburg, NJ). Sodium dodecyl sulfate (SDS), 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS), and octyl-β-d-glucopyranoside were purchased from Sigma-Aldrich (St. Louis, MO). The culturing medium, trypticase soy agar supplemented with 5% sheep blood (TSAB), was purchased from Remel (Lenexa, KS). Sterile inoculation loops were purchased from Copan Diagnostics Inc. (Murrieta, CA). Whatman grade 1 cellulose filter paper was purchased from Whatman International Ltd. (Maidstone, England). Copper clips were purchased from McMasters-Carr (Chicago, IL). 2

3 Microorganism Culturing The bacterial isolates, supplied by biomérieux, Inc. (Hazelwood, MO) were cultured from frozen samples stored at -8 C on TSA with glycerol in cryotubes. All experiments were performed under Purdue University s Institutional Biosafety Committee protocol #7-4-1 "Novel tissue, Biological fluid and Bacteria Evaluation by Mass Spectrometry as amended. Instrumentation The temperature of the MS capillary was set at 275 C. The tube lens voltage was set at - V and V in the negative and positive ion modes, respectively. The capillary voltage was maintained at - V and V in the negative ion mode and positive ion mode, respectively. The Orbitrap instrumental conditions in the negative ion mode were: maximum injection time of ms; two microscans; range of 2 2; activated AGC; 25 V capillary voltage; and 165 V tube lens voltage. Multivariate Statistics Gram-positive Bacteria, Negative mode PS-MS Negative mode PS-MS data matrix consisted of 53 rows and 1681 columns over a reduced mass range 2-1. The negative ion matrix of gram-positive bacteria were further reduced to eliminate unnecessary information, only random noise was detected in this region and it was determined to not affect statistical outcomes. LDA was performed to quantify the separation shown in the PCA score space. LDA was performed after PCA compression by selecting the first 5 PCs (which explain 9% of total data variability) and 5 CV-deletion groups following the cross-validation strategy. Gram-positive Bacteria, Positive mode PS-MS Positive mode PS-MS dataset yielded a data matrix of 51 rows (samples) and 132 columns ( values), over a slightly reduced mass range The positive matrix of gram- 3

4 positive bacteria were further reduced to eliminate unnecessary information, only random noise was detected in this region and it was determined to not affect statistical outcomes. LDA was performed by selecting the first 8 lower-order PCs (that compress 9% of total data variability) and with 5 CV-deletion groups in cross-validation. Gram-negative Bacteria, Negative mode PS-MS PS-MS data from gram-negative bacteria included 68 samples (n 6) collected in both the positive and negative ion modes. Two matrices were built containing 68 rows with the (+) PS- MS matrix containing 156 columns over the mass range 2-1 and the (-) PS-MS matrix containing columns, after removing a window in order to exclude the interfering ion of 649.7, [CHAPS+Cl]- and related isotopic peaks. LDA performed on negative ion matrix, the scores of the first 1 PCs (accounting for about 9% of total data variability), confirms the low predictive ability with an average successful prediction rate of 7.6% (with 5 CV-deletion groups in cross-validation). 4

5 Table S1. List of bacteria that have been investigated using PS-MS Gram Stain Family Species Abbreviation Analytical samples (+) PS-MS / ( ) PS-MS Enterobacteriaceae Proteus penneri PP 6 Enterobacteriaceae Proteus vulgaris PV 7 Enterobacteriaceae Enterobacter aerogenes EA 7 Enterobacteriaceae Enterobacter asburiae EAs 7 Enterobacteriaceae Enterobacter cloacae EC 7 Enterobacteriaceae Citrobacter freundii CFR 7 Enterobacteriaceae Citrobacter farmeri CFA 7 Enterobacteriaceae Escherichia coli EsC 7 Pseudomonadaceae Pseudomonadaceae Pseudomonas aeruginosa Pseudomonas fluorescens PA 6 PF 7 + Staphylococcaceae Staphylococcus aureus SA 7 + Staphylococcaceae Staphylococcus capitis SC 9 / 11 + Staphylococcaceae Staphylococcus lugdunensis SL 1 + Enterococcaceae Enterococcus faecalis EF 1 / 11 + Bacillaceae Bacillus subtilis BS 6 + Bacillaceae Bacillus thuringiensis BT 9 / 8 Table S2. High resolution MS data on particular compounds acquired in negative ion mode using optimized PS-MS method (MeOH with.5% CHAPS) Compound ID Theoretical mass Experimental mass Absolute mass error (ppm) Palmitic acid Stearic acid [CHAPS+Cl-] PG (3:) PG (31:) PG (15:/17:) or PG (17:/15:)** PG (33:2) PG (33:1) PG (33:) PG (34:) PG (35:) ** MS/MS data support chain ID 5

6 Table S3. Gram-positive bacteria. Negative ions (a) CV prediction rates (b) CV confusion matrix for all LDAs (a) CV prediction rates Bacillus subtilis (BS) Bacillus thuringiensis (BT) Enterococcus faecalis (EF) Staphylococcus aureus (SA) 87.5 Staphylococcus capitis (SC) Staphylococcus lugdunensis (SL) (b) LDA on negative ion mode mass spectra Classes BS BT EF SA SC SL BS 6 BT 8 EF 11 SA 7 1 SC 1 SL 1 Table S4. Gram-positive bacteria. Positive ions (a) CV prediction rates (b) CV confusion matrix for all LDAs (a) CV prediction rates Bacillus subtilis (BS) Bacillus thuringiensis (BT) Enterococcus faecalis (EF) 9.9 Staphylococcus aureus (SA) Staphylococcus capitis (SC) Staphylococcus lugdunensis (SL) 9.9 (b) LDA on negative ion mode mass spectra Classes BS BT EF SA SC SL BS 6 BT 9 EF 1 1 SA 7 SC 7 SL 1 1 6

7 Table S5 Gram-negative bacteria. Negative ions (a) CV prediction rates (b) CV confusion matrix for all LDAs (a) CV prediction rates Citrobacter farmeri (CFA) 75 Citrobacter freundii (CFR) 85.7 Enterobacter asburiae (EAS) 66.7 Enterobacter aerogenes (EA) 71.4 Enterobacter cloacae (EC) Escherichia coli (EsC) 83.3 Pseudomonas aeruginsa (PA) Pseudomonas fluorescens (PF) 71.4 Proteus penneri (PP) Proteus vulgaris (PV) 57.1 (b) LDA on negative ion mode mass spectra Classes CFA CFR EAS EA EC EsC PA PF PP PV CFA CFR 1 6 EAS 4 2 EA EC EsC 1 5 PA 6 PF PP PV

8 Table S6. Gram-negative bacteria. Fused datasets (a) CV prediction rates (b) CV confusion matrix for all LDAs. (a) CV prediction rates Citrobacter farmeri (CFA) 87.5 Citrobacter freundii (CFR) Enterobacter asburiae (EAS) Enterobacter aerogenes (EA) Enterobacter cloacae (EC) Escherichia coli (EsC) Pseudomonas aeruginsa (PA) Pseudomonas fluorescens (PF) Proteus penneri (PP) Proteus vulgaris (PV) 85.5 (b) LDA on negative ion mode mass spectra Classes CFA CFR EAS EA EC EsC PA PF PP PV CFA 7 1 CFR 7 EAS 4 4 EA 6 EC 3 3 EsC 7 PA 6 PF 7 PP 5 PV 1 7 8

9 Solvent vol.= 15 µl Spray duration=.96 min R e la ti v e A b u n d a n c e Spray duration=1.4 min Solvent vol.= 2 µl Solvent vol.= 25 µl Spray duration=1.47 min Solvent vol.= 3 µl Spray duration=1.51 min Figure S1. Representative (-) PS-MS spectra of Staphylococcus capitis displaying the optimization of solvent volume. Methanol was utilized as spray solvent; the applied voltage was -3.5kV. 9

10 Figure S2. Average mass spectra obtained by PS-MS obtained in the negative mode of Citrobacter farmeri. 15 µl.5% CHAPS in MeOH was used as spray solvent; the applied spray voltage was -3.5 kv. The peak observed at is attributed to the chloride adduct, [CHAPS+Cl] -. 1

11 11 Figure S3. PCA of negative ions from Gram-positive and Gram-negative bacteria (a) PC1 vs. PC2 score plot. Gram-negative bacteria (red circles, n = 68), Gram-positive bacteria (blue triangles, n = 53). (b) PC1 vs. PC2 loading plot labeled in terms of ratio. (c) PC1 vs. PC2 score plot. Bacteria families: Enterobacteriaceae (blue circles), Pseudomonadaceae (gray circles), Staphylococcaceae (green triangles), Enterococcaceae (black triangles), Bacillaceae (red triangles). (d) PC1 vs. PC2 score plot. Bacterial genera: Citrobacter (black circles), Enterobacter (green circles), Proteus (blue circles), Escherichia (pink circles), Pseudomonas (red circles), Staphylococcus (gray triangles), Enterococcus (magenta triangles), and Bacillus (blue triangles) Scores on PC1 (22.5%) Scores on PC2 (13.4%) SCORE PLOT (a) Loadings on PC1 (22.5%) Loadings on PC2 (13.4%) LOADING PLOT (b) Scores on PC1 (22.5%) Scores on PC2 (13.4%) SCORE PLOT (c) Scores on PC1 (22.5%) Scores on PC2 (13.4%) SCORE PLOT (d)