a report by

J o h n C G e b l e r , J e f f R M a z z e o and Wi l l i am J Wa r r e n

Director, Life Sciences Reasearch and Development, Director, Chemistry Applied Technologies, and

Manager, Chemistry Life Science Marketing, Waters Corporation

Within the last decade, life science investigations haverapidly evolved from research and development(R&D) initiatives to the isolation and characterisationof commercialised biopharmaceutical products. Infact, of all new medicines in active clinical trials, some 27% are biopharmaceuticals.1 This representsapproximately 500 new biopharmaceutical candidatesin clinical evaluation.2 Intensified investigations in theareas of proteomics and biomarker discovery hope toaccelerate the rate of drug discovery. These R&Dinitiatives continue at a wide variety of institutionsincluding academic, small biotech start-ups andinternational pharmaceutical conglomerates. Therealisation of robust, sensitive and accurate liquidchromatography (LC) and mass spectrometry (MS)technologies has been integral to the successfuldevelopment of biopharmaceuticals.

Highly evolved instrumentation and methodologieshave revolutionised the way biopolymers areanalysed. For example, a prominent use of newseparation and detection technologies is centred onpeptide characterisation. In a well-characterisedbiopharmaceutical application, this might involve thesimple determination of peptide purity usingreversed-phase high performance liquidchromatography (HPLC). At the other extreme, theuse of sophisticated hybrid LC/MS systems for thequalitative and quantitative characterisation ofhundreds of peptides contained in a complex proteindigest might be required.

The pace at which new LC and MS technologiesevolve closely mimics the rapid advances seen withconsumer electronic devices and software. Scientificinstruments that push the limit of resolution anddetection have become readily available to thescientific masses. For example, Waters’ Corporationintroduced the ACQUITY UPLC™ System in early2004, which promises to revolutionise the qualityand quantity of information obtained by LC. TheACQUITY UPLC System was specifically designedto take advantage of improvements inchromatographic resolution, sensitivity and speed

afforded by using sub-2µm chromatographic mediain traditional length columns. This integrated andoptimised system solution was extended during thesummer with the introduction of Waters’nanoACQUITY™ system designed as a ‘next-generation’ inlet for advanced MS analyses ofbiocompounds using electrospray ionisation methodsat nano-flowrates.

Nano-flow LC interfaces coupled with highperformance MS systems are necessary to obtain thehigh sensitivity required for the analysis of sample-limited or low abundance biopolymers such aspeptides. Nano chromatography is performed using≤150µm internal diameter HPLC columns operatedat ≤1,000nL/min flows. Initially, many scientistsstudying proteomics became skilled in packing theirown columns. This was done out of necessity sincenano columns packed with high-performancesorbents were not commercially or readily available.In fact, separation sorbents (e.g. C18 reversed-phasematerials) were generally obtained by unpacking apurchased analytical column and repacking thematerial into a nano column format.

Today, laboratory directors, professors, companiesand investors are interested in results; that is, theapplication of advanced LC/MS techniques towardsfinding answers to challenging biological problems.Savings from self-packed nano columns will clearlybe offset when factors such as the time required topack, test and document column performance arecalculated into the total cost of operation. Thus, self-packed columns may be a risky venture whenprecious samples are analysed.

Self-packed columns raise additional concerns intoday’s regulated environment with extensivevalidation and compliance requirements.Fortunately, several companies now offer sub-1mminternal diameter columns for LC/MS applications.For example, Waters’ NanoEase™ capillary, trappingand nano columns containing high performancereversed-phase and ion-exchange sorbents are

The Ro le o f Chemis t r y Consumables in B iopharmaceut i ca l Product Deve lopment

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1. Bibby K, Davis J and Jones C, “Biopharmaceuticals-Moving to Centre Stage” IMS Global Consulting Report, (2003). 2. Walsh G, Nature Biotechnology (2003), 23, pp. 865–870.

available and produced in a fashion similar to thatused for analytical columns (i.e. ≥1mm internaldiameter). State-of-the-art techniques have resultedin commercially available nano columns that haveperformance characteristics equal to those ofanalytical columns (see Figure 1). These analyticaltools have evolved to such a point that laboratoryscientists no longer need to be expertchromatographers in order to realise the synergiesfrom LC/MS methods. Efforts can now beappropriately focused on research activities directedtowards the development of new drugs, improvedtreatment regimes or enhanced diagnosticscapabilities.

Recently, attention has focused on how samplepreparation affects the quality of collected data andinterpreted results for well-characterised proteins.Biopharmaceutical corporations have invested heavilyin acquiring sophisticated scientific instrumentationand informatic technologies. However, the collectedand software-reduced data obtained from thesesystems are only as good as the quality of the analysed

samples. For example, peptide mapping is frequentlyperformed during the investigations directed towardsthe development of a new, protein-basedbiopharmaceutical. A variety of well-documentedchemical and enzymatic methods are used for samplepreparation prior to LC, MS or LC/MS analyses of thegenerated peptides. The use of high-quality trypsin iscommonly employed for protein digestions since thisenzyme normally creates predictable peptidefragments of moderate length based on the amino acidsequence of the target compound. With this simpleand inexpensive reagent, techniques have beendeveloped that take advantage of sophisticatedLC/MS methods such as peptide mass fingerprinting.While many readily soluble proteins are effectivelydigested with trypsin, many proteins of biologicalimportance (e.g. membrane proteins) are resistant todigestion due to their hydrophobic nature. Eventhough hydrophobic proteins can be solubilised priorto digestion, most surfactants significantly inhibitendoprotease activity, which can yield incompletedigestion and poor peptide mass fingerprinting results.Furthermore, it is often necessary to remove the

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Figure 1: Total Ion Count (TIC) Chromatogram of an Enolase Protein Digest on a Waters’ NanoEase™ Nano

Column

10.00 20.00 30.00 40.00 50.00 60.00 70.00 80.00

Time (Min)

0

100

%

Sample: 500 fmol Enolase DigestColumn: Waters NanoEaseTM Capillary Column Symmetry C18, 75 µm x 150 mmEluent A: 0.1% Formic Acid in waterEluent B: 0.1% Formic Acid in acetonitrileGradient: 3 to 60% B in 120 minFlow rate: 250 nl/minSystem: Waters nanoACQUITYTM System with QTof Micro

Figure 2: TIC from LC/MS of Trypsin Digested Bacteriorhodopsin in the Presence of Waters’ RapiGest™ SF

Reagent

15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95

Time

T6

T2

T8

T13

T11

T13

T4

T10

T3-

4 T7

T6-

7

T10

-11

T5

990 992 994 996

m/z

T7 (M+3H)3+

T11

T12

The identified tryptic peptides are labelled which represents about 97% of the amino acid sequence of the protein. Peaks labelled T11 through T13 are N-terminal peptides

with different modifications. No digestion is observed when digestion is attempted with trypsin without RapiGest™ SF.

The Ro le o f Chemis t r y Consumables in B iopharmaceut i ca l Product Deve lopment

denaturants (e.g. sodium dodecyl sulphate (SDS))post-cleavage since surfactants frequently interfere(e.g. ion suppression) with the mass analysis ofbiopolymers. Recent investigations have resulted inthe introduction of novel surfactants that are wellsuited for this demanding application.

Waters’ RapiGest™ SuperFect (SF) reagent is anacid-labile detergent that effectively denaturesproteins and does not interfere with trypsin activity.In addition, the generated peptides are free fromadduct or other modifications that are frequentlyencountered using other protein solubilisationreagents (e.g. carbamylation via the use of urea).Since the RapiGest™ SF reagent is acid-labile (i.e.degraded in the presence of 0.1% trifluoroacetic acid(TFA)), it can easily be removed prior to LC/MS ormatrix-assisted laser desorption time-of-flight(MALDI TOF) analysis. Proteolytic-resistantproteins such as the membrane-boundbacteriorhodopsin is completely digested overnightin the presence of RapiGest™ SF (see Figure 2).Over the past year, several manuscripts featuring thisreagent for simple in-solution digestion, in-geldigestion, membrane protein digestion and wholecell lysate digestion have been published.3–7 On-going investigations support the use of this reagent tosolubilise glycoproteins prior to the enzymaticcleavage of N-linked carbohydrates (see Figure 3).

While peptide mapping is frequently used to analysean isolated protein, applications exist where analytical

data from the intact protein is desired. For example,results from peptide mapping experiments can becorrelated with intact protein analysis to better definethe protein of interest. An especially powerful toolfor intact protein analysis is MS. In theseexperiments, the undigested protein is infused orinjected into a mass spectrometer where themolecular weight is accurately measured. In additionto obtaining an accurate molecular weight for theanalysed protein, mass analysis can also giveinformation on protein modifications, such asglycosylation, oxidation, etc. This information canthen be compared with the peptide mapping data toconfirm the site(s) of modification.

Due to MS using high vacuum sources as part of theionisation and detection technology, it is important tominimise the introduction of non-volatile salts into themass analyser. Salts, if not removed, can suppress theionisation of the analysed intact proteins and lead topoor detection sensitivity. A variety of publishedsample preparation procedures report the use of‘offline’ devices (e.g. Ziptips® C4 from MilliporeCorporation) that can effectively be used to removesalts from the proteins prior to analysis. In an attemptto increase sample throughput in automated LC/MSapplications, Waters introduced its MassPREP™Online Desalting Cartridge (2.1x10mm) for proteindesalting prior to mass spectral analysis.

The MS-compatible, reversed-phase materialcontained in these online devices successfully ‘traps’

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Figure 3: Deconvoluted Spectrum of Ovalbumin Deglycosylated in the Presence of PNGase F and Waters’

RapiGest™ SF (insert, raw spectrum)

0

42946 (deglycosylated ovalbumin)

42866

42816

4456842975 4416243003 44771

41000 42000 43000 44000 45000 46000 47000 48000 49000

Mass

100

%

m/z

minor glycosylatedspecies

raw spectrum

3. Yu Y-Q, Gilar M, Lee P J, Bouvier E S P and Gebler J C, “Enzyme-Friendly, Mass Spectrometry-Compatible Surfactantfor In-Solution Enzymatic Digestion of Proteins”, Anal. Chem. (2003), 75, pp. 6,023–6,028.

4. YYu Y-Q, Gilar M and Gebler J C, “A Complete Peptide Mapping of Membrane Proteins: A Novel Surfactant Aidingthe Enzymatic Digestion of Bacteriorhodopsin”, Rapid Commun. Mass Spectrom. (2004), 18, pp. 711–715.

5. Stover T, Amari J V, Mazsaroff I, Yu Y-Q, Gilar M and Gebler J C, “RapiGest™ SF Denaturant Tool for ImprovedTrypsin Digestion of Monoclonal Antibodies”, Genetic Engineering News (2003), 23, pp. 48–49.

6. Arnold R J, Hrncirova P, Annaiah K and Novotny M V “Fast Proteolytic Digestion Coupled with Organelle Enrichmentfor Proteomic Analysis of Rat Liver”, Journal of Proteome Research (2004), 3, pp. 653–657.

7. Nomura E, Katsuta K, Ueda T, Toriyama M, Mori T and Inagaki N “Acid-labile surfactant improves in-sodiumdodecylsulfate polyacrylamide gel protein digestion for matrix-assisted laser desorption/ionization mass spectrometric peptidemapping”, J. Mass Spectrom. (2004), 39, pp. 202–207.

No deglycosylation was observed when RapiGest was omitted from the PNGase F containing solution.

proteins (e.g. hydrophobic monoclonal antibodies)allowing the salts to be washed to waste prior toelution of the desalted protein onto the massspectrometer for analysis. With an optimised LC/MSmethod, cycle times as low as three minutes areachievable. Of equal importance, is the fact thatWaters’ MassPREP™ Online Desalting Cartridge,when used with an appropriate HPLC systeminjector and injector wash solution, can be used forthe sequential analyses of different samples (e.g. 50 to100 in an overnight method) due to the lack ofprotein carry-over from prior injections.

While inadequate sample preparation can seriouslycompromise the quality of collected data, deficienciesin system or column performance can also seriouslyaffect the quality of results. In today’s pharmaceuticalquality control (QC) laboratories, a series of system andcolumn performance qualification tests are routinelyperformed prior to the analysis of test compounds. Theimportance of performing these tests is significantlyincreased with the analysis of valuable volume andconcentrated limited samples as found in proteomicsand biomarker investigations. A recent article entitled“HPLC Standard Controls as a Requirement inProteomics”8 highlights the importance of usingbiological standards (i.e. peptides) in a performancequalification procedure for proteomics research.

Commercially available peptides (e.g. angiotensin

peptide series) can be purchased to create a useful testsample. However, some investigations require morecomplex test mixtures (e.g. trypsin digests of specificproteins). The generation of reproducible and stabletryptic digests for system and column performancetesting can be problematic. Frequently, the enzymedigested samples contain undigested protein(s), trypsinor large hydrophobic peptides. Ideally, a QC-certifiedstandard contains only peptides.

To address this need, in 2003, Waters introduced theMassPREP™ Peptide and Protein DigestionStandards (see Figure 4). These samples are producedusing highly reproducible digestion methods thatyield high-quality standards free of artifactcomponents. They are QC-tested prior tolyophilisation, packaged to maximise stability andshipped with certificates of analyses fordocumentation archives. In addition to high qualitystandards, a variety of MassPREP™ MALDImatrices are purified, QC-tested and packaged toprovide reproducible MALDI TOF analysis ofimportant, concentration limited samples. Incombination, the availability and use of high qualitypeptide, protein digests and MALDI matrices canreduce the time and associated expense in preparingthese important chemistry consumables prior to theanalysis of extremely valuable samples.

Today’s biopharmaceutical organisations have

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Figure 4: TIC of Waters’ MassPREP™ Enolase Digestion Standard Noting the Identified Tyrpsin Cleavage

Peptides

T6

T28

T24T46

T2

T12

T9T19

T5T10

T18T23

T50 T22

T4

T32T42T43

T51

T11

T44

T38

T16

T14

T30

T35

T45

T37

10.00 20.00 30.00 40.00 50.00

T3T47

T40

Time (min)

8. Wefr T, “HPLC Standard Controls as a Requirement in Proteomics”, LCGC North America (2004), 22, pp. 354–361.

The Ro le o f Chemis t r y Consumables in B iopharmaceut i ca l Product Deve lopment

invested heavily in instrumentation (e.g. highperformance LC (HPLC), MS and LC/MS) and havetrained staff to accelerate the discovery anddevelopment of new therapeutic and diagnosticproducts. Obtaining chromatograph resolution ofcomplex biological mixtures at MS-compatible flows,generating quality digests from isolated proteins,removing interfering substances prior to high-throughput MS analysis and assuring proper system,column and method performance prior to theanalyses of valuable samples are some of thefrequently overlooked yet important factors that affect

the quality of generated data and interpreted results. Scientific instrument, software and chemistrymanufacturers such as Waters Corporation arepaying careful attention to the details responsiblefor the successful realisation of reproducible,sensitive and faster analytical methods. Inparticular, this article highlights the importance ofusing high-quality chemistry consumables as part ofa ‘total integrated system solution’, which willmaximise return on investment and help achievebiopharmaceutical research, development andcommercial objectives. ■

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High Quality MS and LC/MS Results

Visit us at www.waters.com/lifesciences to learn more about our complete portfolio of MS and LC/MS products, including:

• RapiGest™ SF Reagent • NanoEase™ Columns

• MassPREP™ Standards and Matrices • 1-D and 2-D Kits for LC/MS

©2004 Waters Corporation. Waters, RapiGest SF, MassPREP, and NanoEase are trademarks of Waters Corporation.

The NanoEase™ column family consists of capillary, nano and trapping formats that utilize several of Waters' premier, mass

spec compatible separations media. These columns help scientists separate, concentrate, fractionate or desalt sample-limited,

complex samples in either 1-D or 2-D LC/MS applications. To ensure optimal system performance prior to the analyses of

your valuable samples, we recommend the routine use of Waters' MassPREP™ Peptide and Protein Digestion Standards.

Waters is an international leader in the development of reagents and chromatography-based technologies for the isolation and characterization of biomolecules. Whether you are using LC/MS or gel electrophoresis with MALDI techniques, Waters has mass spectrometry consumables that will improve the quality of your results.

MassPREP™ Protein Digest Standards

NanoEase™ Capillary Columns

NanoEase™ Nano Columns

NanoEase™ Trapping Columns

T31

10.00 15.00 20.00 25.00 30.00 35.00 40.00 45.00Time0

T7T12T14

T60T102

T4

T87T109

T48

T13

T81T100T106

T57T83

T27T55

T74

T43

T93 T80T49

T52TT7700TT4444

T40

T58

T5T45

T88

T23

T94

T41

T25 T46

T29

T34

T24T91

T59

T32T39 T90

T105

T104

T10T38

T103

T30

T92

T22

T28

T42

T8T107

T54

T47T98

T11T86

T84

T20

T63T65

T62

720001035EN