Clinical MALDI mass spectrometry for tuberculosis diagnostics: speculating the methodological blueprint and contemplating the obligation to improvise

Abstract MALDI MS with its long history in clinical analysis, is a vital tool, well known for its versatility, rapidity and implementation ease. In tuberculosis research, MALDI has outstanding contributions on the pathogen detection aspect as well as disease diagnosis prospect. This article reviews the existing methods and achievements made employing MALDI MS in tuberculosis research. The challenges confronting and limiting MALDI MS based tuberculosis analysis are presented. An interesting yet intriguing lacuna is that almost none of the state-of-art MALDI MS variants, such as DIOS, NIMS, NALDI, NAPA have been implicated into MALDI based tuberculosis research. These nanoplatforms holding fabulous claims for pushing the limits of detection and avoiding matrix interferences, enhanced resolution, being kept away from this research arena is disturbing and is called to notice through this review.

[1]  A. Fateh,et al.  Proteomic analysis of drug-resistant Mycobacterium tuberculosis by one-dimensional gel electrophoresis and charge chromatography , 2016, Archives of Microbiology.

[2]  T. Kim,et al.  The impact of protein extraction protocols on the performance of currently available MALDI-TOF mass spectrometry for identification of mycobacterial clinical isolates cultured in liquid media. , 2016, Clinica chimica acta; international journal of clinical chemistry.

[3]  M. Ferrer-Navarro,et al.  Implementation of MALDI-TOF MS technology for the identification of clinical isolates of Mycobacterium spp. in mycobacterial diagnosis , 2015, European Journal of Clinical Microbiology & Infectious Diseases.

[4]  M. Drancourt,et al.  Direct matrix-assisted laser desorption ionisation time-of-flight mass spectrometry identification of mycobacteria from colonies , 2016, European Journal of Clinical Microbiology & Infectious Diseases.

[5]  M. Doyle,et al.  Matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) mass spectrometry (MS) for the identification of mycobacteria from MBBacT ALERT 3D liquid cultures and Lowenstein–Jensen (LJ) solid cultures , 2014, Journal of Clinical Pathology.

[6]  Sarman Singh,et al.  Comparative proteomic analysis of sequential isolates of Mycobacterium tuberculosis from a patient with pulmonary tuberculosis turning from drug sensitive to multidrug resistant , 2015, The Indian journal of medical research.

[7]  E. Diamandis Mass Spectrometry as a Diagnostic and a Cancer Biomarker Discovery Tool , 2004, Molecular & Cellular Proteomics.

[8]  V. Maurya,et al.  Suppression of Eis and expression of Wag31 and GroES in Mycobacterium tuberculosis cytosol under anaerobic culture conditions. , 2014, Indian journal of experimental biology.

[9]  Jie Wang,et al.  Identification of putative biomarkers for the serodiagnosis of drug-resistant Mycobacterium tuberculosis , 2012, Proteome Science.

[10]  Fu-Quan Yang,et al.  Diagnostic serum proteomic analysis in patients with active tuberculosis. , 2012, Clinica chimica acta; international journal of clinical chemistry.

[11]  J. Starck,et al.  Comparative proteome analysis of Mycobacterium tuberculosis grown under aerobic and anaerobic conditions. , 2004, Microbiology.

[12]  A. Marcsik,et al.  Bone tuberculosis in Roman Period Pannonia (western Hungary). , 2012, Memórias do Instituto Oswaldo Cruz.

[13]  Jicheng Li,et al.  Comparative proteomic analysis of serum diagnosis patterns of sputum smear-positive pulmonary tuberculosis based on magnetic bead separation and mass spectrometry analysis. , 2015, International journal of clinical and experimental medicine.

[14]  V. Govorun,et al.  Molecular characteristics of rifampicin- and isoniazid-resistant Mycobacterium tuberculosis isolates from the Russian Federation. , 2007, The Journal of antimicrobial chemotherapy.

[15]  R. Lipson,et al.  Insights into Desorption Ionization on Silicon (DIOS) , 2013 .

[16]  Meng-Rui Lee,et al.  Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Can Accurately Differentiate between Mycobacterium masilliense (M. abscessus subspecies bolletti) and M. abscessus (Sensu Stricto) , 2013, Journal of Clinical Microbiology.

[17]  M. Lata,et al.  Proteomic analysis of ofloxacin-mono resistant Mycobacterium tuberculosis isolates. , 2015, Journal of proteomics.

[18]  Y. SwarnaNantha A review of tuberculosis research in malaysia. , 2014 .

[19]  Li-zhou Fang,et al.  Proteomic pilot study of tuberculosis pleural effusion. , 2015, Bio-medical materials and engineering.

[20]  M. Baker Mass spectrometry for biologists , 2010, Nature Methods.

[21]  K. Isselbacher,et al.  Isovaleric acidemia: a new genetic defect of leucine metabolism. , 1966 .

[22]  N. Cioffi,et al.  Mechanisms of Nanophase-Induced Desorption in LDI-MS. A Short Review , 2017, Nanomaterials.

[23]  M. Herbster,et al.  Identification of diagnostic markers for tuberculosis by proteomic fingerprinting of serum , 2006, The Lancet.

[24]  Yi Yao,et al.  Identification of serum biomarkers for lung cancer using magnetic bead-based SELDI-TOF-MS , 2011, Acta Pharmacologica Sinica.

[25]  C. Banwell,et al.  Impairment of IFN-Gamma Response to Synthetic Peptides of Mycobacterium tuberculosis in a 7-Day Whole Blood Assay , 2013, PloS one.

[26]  A. Raja,et al.  Multiplex analysis of cytokines/chemokines as biomarkers that differentiate healthy contacts from tuberculosis patients in high endemic settings. , 2013, Cytokine.

[27]  D. Sharma,et al.  An efficient and rapid method for enrichment of lipophilic proteins from Mycobacterium tuberculosis H37Rv for two‐dimensional gel electrophoresis , 2016, Electrophoresis.

[28]  Jian-Min Zhou,et al.  New serum biomarkers for detection of tuberculosis using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry , 2011, Clinical chemistry and laboratory medicine.

[29]  U. Schaible,et al.  Protein identification and tracking in two‐dimensional electrophoretic gels by minimal protein identifiers , 2004, Proteomics.

[30]  S. H. Kaufmann,et al.  Analysis of protein species differentiation among mycobacterial low-Mr-secreted proteins by narrow pH range Immobiline gel 2-DE-MALDI-MS. , 2014, Journal of proteomics.

[31]  W. Sougakoff,et al.  Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry-Based Single Nucleotide Polymorphism Genotyping Assay Using iPLEX Gold Technology for Identification of Mycobacterium tuberculosis Complex Species and Lineages , 2011, Journal of Clinical Microbiology.

[32]  Florentino Fernández Riverola,et al.  Rapid development of proteomic applications with the AIBench framework , 2011, J. Integr. Bioinform..

[33]  Matthew D. Zimmerman,et al.  The association between sterilizing activity and drug distribution into tuberculosis lesions , 2015, Nature Medicine.

[34]  D. Chatterji,et al.  Identification, Activity and Disulfide Connectivity of C-di-GMP Regulating Proteins in Mycobacterium tuberculosis , 2010, PloS one.

[35]  Yong-Hak Kim,et al.  Crystal structure and functional implications of LprF from Mycobacterium tuberculosis and M. bovis. , 2014, Acta crystallographica. Section D, Biological crystallography.

[36]  D. Raoult,et al.  Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Identification of Mycobacteria in Routine Clinical Practice , 2011, PloS one.

[37]  N. Fujiwara,et al.  Characterization of Mycolic Acids in Total Fatty Acid Methyl Ester Fractions from Mycobacterium Species by High Resolution MALDI-TOFMS. , 2015, Mass spectrometry.

[38]  Bernd Thiede,et al.  Assembling proteomics data as a prerequisite for the analysis of large scale experiments , 2009, Chemistry Central journal.

[39]  Qiang Huang,et al.  Altered protein expression patterns of Mycobacterium tuberculosis induced by ATB107 , 2010, The Journal of Microbiology.

[40]  Richard M Caprioli,et al.  Absolute Quantitative MALDI Imaging Mass Spectrometry: A Case of Rifampicin in Liver Tissues. , 2016, Analytical chemistry.

[41]  G. Glish,et al.  The basics of mass spectrometry in the twenty-first century , 2003, Nature Reviews Drug Discovery.

[42]  G. Larrouy-Maumus,et al.  Mycobacterial envelope lipids fingerprint from direct MALDI-TOF MS analysis of intact bacilli. , 2015, Tuberculosis.

[43]  S. Swaminathan,et al.  Pediatric tuberculosis: global overview and challenges. , 2010, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[44]  C. Burnham,et al.  Comparison of Sample Preparation Methods, Instrumentation Platforms, and Contemporary Commercial Databases for Identification of Clinically Relevant Mycobacteria by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry , 2015, Journal of Clinical Microbiology.

[45]  R. Caprioli,et al.  In situ mass spectrometry of autoimmune liver diseases , 2011, Cellular and Molecular Immunology.

[46]  S. Zhang,et al.  Proteomic analysis of sputum in patients with active pulmonary tuberculosis. , 2012, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[47]  N. Singhal,et al.  Streptomycin induced protein expression analysis in Mycobacterium tuberculosis by two-dimensional gel electrophoresis & mass spectrometry. , 2010, The Indian journal of medical research.

[48]  I. Blair,et al.  Mass spectrometry-based approaches to targeted quantitative proteomics in cardiovascular disease , 2016, Clinical Proteomics.

[49]  U. Singh,et al.  Rapid identification of clinical mycobacterial isolates by protein profiling using matrix assisted laser desorption ionization-time of flight mass spectrometry. , 2013, Indian journal of medical microbiology.

[50]  P. Berche,et al.  Rapid Identification of Mycobacterial Whole Cells in Solid and Liquid Culture Media by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry , 2010, Journal of Clinical Microbiology.

[51]  J. C. Sundaramurthi,et al.  Immunological and proteomic analysis of preparative isoelectric focusing separated culture filtrate antigens of Mycobacterium tuberculosis. , 2010, Experimental and molecular pathology.

[52]  Michelle L. Reyzer,et al.  Reagent Precoated Targets for Rapid In-Tissue Derivatization of the Anti-Tuberculosis Drug Isoniazid Followed by MALDI Imaging Mass Spectrometry , 2011, Journal of the American Society for Mass Spectrometry.

[53]  J. Belisle,et al.  Immunoproteomic Identification of Human T Cell Antigens of Mycobacterium tuberculosis That Differentiate Healthy Contacts from Tuberculosis Patients* , 2009, Molecular & Cellular Proteomics.

[54]  Hui-Fen Wu,et al.  State‐of‐the‐art nanoplatform‐integrated MALDI‐MS impacting resolutions in urinary proteomics , 2015, Proteomics. Clinical applications.

[55]  Sandeep Kumar,et al.  Cloning, expression, purification and crystallization of a transcriptional regulatory protein (Rv3291c) from Mycobacterium tuberculosis H37Rv. , 2004, Acta crystallographica. Section D, Biological crystallography.

[56]  G. Bai,et al.  Antigens secreted from Mycobacterium tuberculosis: Identification by proteomics approach and test for diagnostic marker , 2004, Proteomics.

[57]  N. Singhal,et al.  Analysis of intracellular expressed proteins of Mycobacterium tuberculosis clinical isolates , 2012, Proteome Science.

[58]  Brendan Prideaux,et al.  High-sensitivity MALDI-MRM-MS imaging of moxifloxacin distribution in tuberculosis-infected rabbit lungs and granulomatous lesions. , 2011, Analytical chemistry.

[59]  Inhibition of Mycobacterium tuberculosis PknG by non-catalytic rubredoxin domain specific modification: reaction of an electrophilic nitro-fatty acid with the Fe-S center. , 2013, Free radical biology & medicine.

[60]  M. Lata,et al.  Comparative Proteomic Analysis of Aminoglycosides Resistant and Susceptible Mycobacterium tuberculosis Clinical Isolates for Exploring Potential Drug Targets , 2015, PloS one.

[61]  Jen-Jyh Lee,et al.  Validation of nanodiamond-extracted CFP-10 antigen as a biomarker in clinical isolates of Mycobacterium tuberculosis complex in broth culture media. , 2015, Tuberculosis.

[62]  M. Zimmerman,et al.  Mass spectrometry imaging of levofloxacin distribution in TB-infected pulmonary lesions by MALDI-MSI and continuous liquid microjunction surface sampling. , 2015, International journal of mass spectrometry.

[63]  N. Singhal,et al.  Proteomic analysis of streptomycin resistant and sensitive clinical isolates of Mycobacterium tuberculosis , 2010, Proteome Science.

[64]  Jicheng Li,et al.  The discovery and identification of a candidate proteomic biomarker of active tuberculosis , 2013, BMC Infectious Diseases.

[65]  R. Koski,et al.  Inhibition of mycobacterial alanine racemase activity and growth by thiadiazolidinones. , 2013, Biochemical pharmacology.

[66]  L. Pucillo,et al.  Determination of antituberculosis drug concentration in human plasma by MALDI‐TOF/TOF , 2010, IUBMB life.

[67]  K. Niitsuma,et al.  [Identification of mycobacteria by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry--using reference strains and clinical isolates of Mycobacterium]. , 2014, Kekkaku : [Tuberculosis].

[68]  Sebastian Böcker,et al.  Novel Mass Spectrometry-Based Tool for Genotypic Identification of Mycobacteria , 2004, Journal of Clinical Microbiology.

[69]  Martine Guillerm,et al.  Tuberculosis Diagnosis and Drug Sensitivity Testing: An Overview of the Current Diagnostic Pipeline , 2006 .

[70]  V. Sabareesh,et al.  Mass spectrometry based lipid(ome) analyzer and molecular platform: a new software to interpret and analyze electrospray and/or matrix-assisted laser desorption/ionization mass spectrometric data of lipids: a case study from Mycobacterium tuberculosis. , 2013, Journal of mass spectrometry : JMS.

[71]  Ji Yue,et al.  Serum Protein Profiling of Smear-Positive and Smear-Negative Pulmonary Tuberculosis Using SELDI-TOF Mass Spectrometry , 2009, Lung.

[72]  M. Drancourt,et al.  Long-term survival of tuberculosis complex mycobacteria in soil. , 2014, Microbiology.

[73]  Young Kil Park,et al.  Comparative proteomic analysis of virulent Korean Mycobacterium tuberculosis K-strain with other mycobacteria strain following infection of U-937 macrophage. , 2007, Journal of microbiology.

[74]  Hongtao Li,et al.  Discovery and verification of serum differential expression proteins for pulmonary tuberculosis. , 2015, Tuberculosis.

[75]  Thomas Deufel,et al.  Use of SELDI-TOF mass spectrometry for identification of new biomarkers: potential and limitations. , 2007, Clinical chemistry and laboratory medicine.

[76]  Jen-Jyh Lee,et al.  Detonation nanodiamonds for rapid detection of clinical isolates of Mycobacterium tuberculosis complex in broth culture media. , 2012, Analytical chemistry.

[77]  G. Siuzdak,et al.  Nanostructure-initiator mass spectrometry: a protocol for preparing and applying NIMS surfaces for high-sensitivity mass analysis , 2008, Nature Protocols.

[78]  Jicheng Li,et al.  Screening and identification of potential biomarkers and establishment of the diagnostic serum proteomic model for the Traditional Chinese Medicine Syndromes of tuberculosis. , 2014, Journal of ethnopharmacology.

[79]  B. Thibeault,et al.  Laser desorption ionization (LDI) silicon nanopost array chips fabricated using deep UV projection lithography and deep reactive ion etching , 2015 .

[80]  Robert C. Walchak,et al.  Evaluation of Matrix-Assisted Laser Desorption Ionization−Time of Flight Mass Spectrometry for Identification of Mycobacterium species, Nocardia species, and Other Aerobic Actinomycetes , 2015, Journal of Clinical Microbiology.

[81]  M. Zimmerman,et al.  Statin adjunctive therapy shortens the duration of TB treatment in mice. , 2016, The Journal of antimicrobial chemotherapy.

[82]  D. Sharma,et al.  Proteomic analysis of Mycobacterium tuberculosis isolates resistant to kanamycin and amikacin. , 2013, Journal of proteomics.

[83]  Y. Wang,et al.  Comparison of Heat Inactivation and Cell Disruption Protocols for Identification of Mycobacteria from Solid Culture Media by Use of Vitek Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry , 2013, Journal of Clinical Microbiology.

[84]  M. Lata,et al.  Proteome analysis of ofloxacin and moxifloxacin induced mycobacterium tuberculosis isolates by proteomic approach. , 2015, Protein Peptide Letters.

[85]  J. Chu,et al.  Differential Levels of Alpha-2-Macroglobulin, Haptoglobin and Sero-Transferrin as Adjunct Markers for TB Diagnosis and Disease Progression in the Malnourished Tribal Population of Melghat, India , 2015, PloS one.