Andrew J Alpert1, Otto Hudecz2,3, Karl Mechtler2,3. 1. †PolyLC Inc., 9151 Rumsey Road, Ste. 175, Columbia, Maryland 21045, United States. 2. ‡Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, 1030 Vienna, Austria. 3. §Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
Abstract
Most phosphoproteomics experiments rely on prefractionation of tryptic digests before online liquid chromatography-mass spectrometry. This study compares the potential and limitations of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) and anion-exchange chromatography (AEX). At a pH higher than 5, phosphopeptides have two negative charges per residue and are well-retained in AEX. However, peptides with one or two phosphate groups are not separated from peptides with multiple Asp or Glu residues, interfering with the identification of phosphopeptides. At a pH of 2, phosphate residues have just a single negative charge but Asp and Glu are uncharged. This facilitates the separation of phosphopeptides from unmodified acidic peptides. Singly phosphorylated peptides are retained weakly under these conditions, due to electrostatic repulsion, unless hydrophilic interaction is superimposed in the ERLIC mode. Weak anion-exchange (WAX) and strong anion-exchange (SAX) columns were compared, with both peptide standards and a HeLa cell tryptic digest. The SAX column exhibited greater retention at pH 6 than did the WAX column. However, only about 60% as many phosphopeptides were identified with SAX at pH 6 than via ERLIC at pH 2. In one ERLIC run, 12 467 phosphopeptides were identified, including 4233 with more than one phosphate. We conclude that chromatography of phosphopeptides is best performed at low pH in the ERLIC mode. Under those conditions, the performances of the SAX and WAX materials were comparable. The data have been deposited with the ProteomeXchange with identifier PXD001333.
Most phosphoproteomics experiments rely on prefractionation of tryptic digests before online liquid chromatography-mass spectrometry. This study compares the potential and limitations of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) and anion-exchange chromatography (AEX). At a pH higher than 5, phosphopeptides have two negative charges per residue and are well-retained in AEX. However, peptides with one or two phosphate groups are not separated from peptides with multiple Asp or Glu residues, interfering with the identification of phosphopeptides. At a pH of 2, phosphate residues have just a single negative charge but Asp and Glu are uncharged. This facilitates the separation of phosphopeptides from unmodified acidic peptides. Singly phosphorylated peptides are retained weakly under these conditions, due to electrostatic repulsion, unless hydrophilic interaction is superimposed in the ERLIC mode. Weak anion-exchange (WAX) and strong anion-exchange (SAX) columns were compared, with both peptide standards and a HeLa cell tryptic digest. The SAX column exhibited greater retention at pH 6 than did the WAX column. However, only about 60% as many phosphopeptides were identified with SAX at pH 6 than via ERLIC at pH 2. In one ERLIC run, 12 467 phosphopeptides were identified, including 4233 with more than one phosphate. We conclude that chromatography of phosphopeptides is best performed at low pH in the ERLIC mode. Under those conditions, the performances of the SAX and WAX materials were comparable. The data have been deposited with the ProteomeXchange with identifier PXD001333.
The reversible phosphorylation
of proteins on serine, threonine, and tyrosine residues is one of
the most prominent regulatory mechanisms in biology. Consequently,
analysis of this important post-translational modification with mass
spectrometry (MS) is a central piece in the proteomics toolbox. Phosphopeptides
tend to be of low abundance in complex tryptic digests. To achieve
high coverage of the phosphoproteome, specific enrichment and prefractionation
of phosphopeptides is required before online liquid chromatography-tandem
MS (LC-MS/MS). Several protocols exploit the charge difference between
phosphorylated and nonphosphorylated peptides. One such technique,
AEX, is increasingly being used for the isolation of phosphopeptides
from tryptic digests.[1−5] However, at low pH AEX is unsuited for the isolation of singly phosphorylated
tryptic peptides. The electrostatic attraction conferred by a single
phosphate group does not suffice to compensate for the electrostatic
repulsion of the two basic groups inherent to most tryptic peptides:
the N-terminus and the side-chain amino group of the C-terminal amino
acid. Consequently, most tryptic phosphopeptides elute from AEX columns
in or near the void volume at low pH.[6] Phosphopeptides
that are retained under these conditions tend to contain additional
acidic residues.[2,7] Two different analytical strategies,
electrostatic repulsion–hydrophilic interaction chromatography
(ERLIC) and AEX at high pH, can be employed to address this limitation.In the case of ERLIC, the mobile phase contains more than 60% acetonitrile
(ACN), leading to additional hydrophilic interaction superimposed
on the electrostatic effects.[8] The combination
of the hydrophilic interaction of phosphate groups plus their electrostatic
attraction to anion-exchange material suffices to separate them from
most of the unmodified peptides even in complex tryptic peptide mixtures.
ERLIC has been used successfully for the isolation of phosphopeptides
in a number of studies.[9−17] When the same phosphopeptide enrichment (IMAC or titania) method
is used for fractions from either SCX or ERLIC, then considerably
more phosphopeptides are identified via ERLIC.[18] Off-line enrichment employing either titania or IMAC material
is important because acidic unmodified peptides tend to coelute with
phosphopeptides and then suppress the ionization of the phosphopeptides
in mass spectrometry. Getting rid of the acidic unmodified peptides
increases dramatically the number of phosphopeptides identified.[19,20] The problem with acidic unmodified peptides is minimized by performing
the chromatography at pH values of around 2.0, leaving carboxyl groups
mostly uncharged.A competing strategy uses AEX material at
a pH higher than 6. In
this case, phosphate groups acquire a second negative charge. That
increases their retention, making AEX of singly phosphorylated tryptic
peptides practical. Some studies involved a pH in the range 7–8,[1,4,21] while other protocols used initial
pH values as high as 9–10.[3,5] High pH conditions
impose two constraints upon the chromatographic conditions. First,
weak anion-exchange (WAX) materials lose overall charge density in
a continuum between pH 5 and 9.5[22] while
strong anion-exchange (SAX) materials maintain their charge density
over that range. Accordingly, all reported separations at high pH
conditions have been performed with SAX materials. Second, silica
dissolves at pH higher than 8. Accordingly, all of the work in that
range has involved polymeric materials. The most frequently reported
material is POROS HQ, while many reports merely cite the use of a
SAX material with no further details.Although WAX materials
exhibit lower retention times than SAX materials
at high pH conditions, the retention may still be adequate for the
purpose. Additionally, the selectivity for certain analytes could
conceivably be better. This is important because the carboxyl groups
of acidic peptides are fully charged under these conditions. While
the majority of tryptic phosphopeptides have a single phosphate group,
unmodified peptides may contain numerous Asp and Glu residues; therefore,
phosphopeptide enrichment methods should at the least be able to separate
singly phosphorylated peptides from peptides with 2–3 acidic
residues. The ability to distinguish between these categories has
been assessed to some extent with some of the combinations listed
above[2,3] but not in a comparison of WAX versus SAX.
Also, while the particular electrolytes used in the mobile phase have
been shown to have a major effect on selectivity for phosphopeptides
in the ERLIC mode,[8] this has not been studied
in the AEX mode. The goal of this study is to systematically optimize
the selective isolation of tryptic phosphopeptides for phosphoproteomic
studies. Toward this end, we assess the retentivity and selectivity
of SAX and WAX materials for phosphopeptide separations, with special
attention to the separation of phosphopeptides from acidic nonphosphorylated
peptides over a wide pH range. Finally, we address the effects of
using different salts for the separations.
Materials and Methods
Materials
PolyWAX LP, a commercial product of PolyLC
Inc. (Columbia, MD), was synthesized via an adsorbed, cross-linked
coating of linear polyethylenimine largely as described.[22] The material was made with the standard commercial
coating applied to a silica that had been synthesized via a process
that makes it resist attack at pH 9.0–9.5 in case it was necessary
to study performance in that range. PolySAX LP, an experimental material,
was prepared by quaternizing the PolyWAX LP material with methyl groups
in a manner similar to that described by Regnier and co-workers.[23,24]
Reagents
The peptides WAGGDASGK and WAGG(pS)ASGK were
purchased from California Peptide Research (Napa, CA). WWGSGPSGSGGSGGGK
and its analogues phosphorylated on Ser were synthesized in-house
by Mathias Madalinski (IMP, Vienna) or were a gift of Goran Mitulović
(Medical University of Vienna). Analogues of WWGSGPSGSGGSGGGK with
Asp substituted for Ser were purchased from United Biosystems (Cabin
John, MD).All other reagents were from Sigma-Aldrich (St. Louis).
Mobile Phase Preparation
Salt buffers were prepared
by dissolving a known quantity of the acid in water and titrating
with the base to attain the desired pH (example: dissolving high-performace
liquid chromatography (HPLC)-grade H3PO4 in
water and titrating with KOH or triethylamine). This was measured
prior to addition of ACN, after which no measurement or adjustment
of pH was performed.
HeLa Sample Preparation
HeLa Kyoto cells were grown
in Dulbecco's modified Eagle's medium. Mitosis was arrested
with nocodazol
treatment overnight. They were then harvested and lysed with freshly
prepared 8 M urea and the protein concentration was measured using
a Bradford assay. The lysate was reduced and alkylated with dithiothreitol
and iodoacetamide and then digested with Lys-C and Trypsin. Peptides
were enriched from the digestion mixture using reversed-phase (RP)
C18 Sep-Pak cartridges (Waters) and the eluate was dried to completion
in a vacuum centrifuge.
Phosphopeptide Enrichment
HPLC separation
was performed
on an UltiMate 3000 (Dionex) equipped with a fraction collector. Eight
hundred micrograms of the peptide mixture was fractionated on either
a PolySAX LP or PolyWAX LP column (PolyLC; 4.6 mm inner diameter (i.d.)
× 200 mm, 5 μm particle size, 300 Å) using a binary
solvent system of solvent A (for ERLIC separations: 70% acetonitrile,
20 mM sodium methylphosphonate, pH 2.0; for AEX separation: 10% acetonitrile,
20 mM ammonium acetate, pH 6.0) and solvent B (10% acetonitrile, 300
mM triethylammonium phosphate, pH 2.0) delivered at 1 mL/min per the
following linear gradient: 5 min at solvent A, then 43 min to 100%
solvent B, and then 5 min at 100% solvent B. Fractions were collected
every 1 min between 0 and 50 min. Every two adjacent fractions were
pooled. ACN was removed by drying to half the original volume. This
was followed by desalting using RP-C18 Sep-Pak cartridges. The eluates
were dried to completion in a vacuum centrifuge.
LC-MS/MS Analysis
Nano-HPLC-MS/MS was performed on
an UltiMate 3000 RSLCnano (Dionex) coupled online to a Q-Exactive
(Thermo Fisher Scientific). Fractions were first loaded onto a RP-C18
trap column (Acclaim PepMap Nano-Trap, Dionex; 100 μm i.d. ×
100 mm, 5 μm particle size, 300 Å pore size) using 25 μL/min
solvent C (0.1% trifluoroacetic acid in water) and then separated
on a RP C18 column (Acclaim PepMap RSLC, Dionex; 75 μm i.d.
× 500 mm, 2 μm particle size, 100 Å pore size) using
a binary solvent system of solvent D (0.1% formic acid in water) and
solvent E (80% acetonitrile and 0.1% formic acid in water) delivered
at 230 nL/min in one of the following linear gradients: 10 min at
2% solvent D, in 60 min (1 h gradient) or 120 min (2 h gradient) to
35% solvent D, in 5 min to 90% solvent D, 5 min at 90% solvent D.
Peptides were ionized by electrospray using coated nanospray emitters
(SilicaTip, New Objective; 10 μm tip i.d.) biased to 1.9 kV.
The mass spectrometer was operated in data-dependent acquisition mode
with one MS scan followed by 15 sequential MS/MS scans of the most
intense precursors. Airborne dodecamethylhexacyclosiloxane was used
as lockmass. The MS scan was acquired from 350 to 2000 m/z at a resolution of 70 000, an automatic
gain control (AGC) target value of 1 000 000 and a maximal
injection time (IT) of 50 ms. Precursor ions with a charge >1 and
an intensity >100 000 were selected for MS/MS, which was
performed
with an isolation width of 2 m/z and a HCD normalized collision energy of 27. The MS/MS scan was
acquired at a resolution of 17 500 with a dynamic m/z range, an AGC target value of 100 000,
and a maximal IT of 200 ms. Fragmented precursor ions were excluded
from fragmentation for 30 s.
Data Analysis
For peptide identification,
the.RAW-files
were loaded into Proteome Discoverer (Thermo Fisher Scientific; version
1.4.0.288). All MS/MS spectra created thereby were searched using
MS Amanda[25] against the Swiss-Prot human
protein sequence database (www.uniprot.org; retrieved June
29, 2014; 20 581 entries). The following search parameters
were used: carbamidomethylation on cysteine was set as a fixed modification
and oxidation on methionine was set as a variable modification as
was phosphorylation of serine, threonine, and tyrosine. Monoisotopic
masses were searched within unrestricted protein masses for tryptic
peptides. The peptide mass tolerance was set to ±8 ppm and the
fragment mass tolerance to ±20 ppm. The maximal number of missed
cleavages was set to 2. The result was filtered to 1% false discovery
rate using the Percolator algorithm[26] integrated
in Proteome Discoverer. Numbers are reported for unique peptide sequences
as well as for peptide spectrum matches. PhosphoRS was applied for
phosphorylation site probability estimation for every phosphorylated
peptide spectrum match.[27] No threshold
was defined since this may decrease identification of multiphosphorylated
peptides. It is more difficult to localize their positions of phosphorylation,
especially when multiple accessor sites are in close proximity. The
focus in this paper was the chromatography behavior of peptides with
one or more phosphate groups under different conditions and with different
materials, not defining the exact position of phosphorylation of multiphosphorylated
peptides.
Results
Generation
of Column Materials
The silica used for
this study was synthesized using a process that imparts some degree
of resistance to attack in the pH range 9–9.5. The WAX material
was prepared by adsorption of linear polyethylenimine to the surface
with subsequent cross-linking of the adsorbed polymer to form a macromolecular
network that envelopes the silica particle inside the pores and out.
The lack of a silane coating increases the resistance to loss of capacity
at elevated pH. The SAX material was formed by quaternization of the
WAX material with methyl groups. Going by the data below, we estimate
that about 70% of the amine residues in the resulting SAX material
are quaternary (4°), the rest being some combination of primary
(1°), secondary (2°), and tertiary (3°) amines. This
is consistent with the silica-based materials prepared by Regnier
and co-workers using a similar process.[23,24] Titration
data suggest that the POROS HQ material, widely used by groups currently
isolating phosphopeptides, also has about 60% content of 4° amines,[28] the rest being 1°, 2°, or 3°.
This range of 60–70% for 4° amine residues appears to
be a mark of SAX materials made by quaternization of WAX materials.
SAX materials made through processes that can only result in a 4°
amine (e.g., reaction of trimethylamine with an immobilized alkyl
bromide) are readily distinguished by their titration curves.[28,29] It is not evident that complete quaternization of the stationary
phase is necessary or even desirable for this application. Drager
and Regnier have reported that optimum selectivity for some oligonucleotide
separations was obtained with materials that were 40–60% quaternized.[24] That is not necessarily true for smaller solutes
such as tryptic peptides that may have only one or two acidic residues.
It is beyond the scope of the present study to ascertain the importance
to peptideAEX of the extent of quaternization.
Impact of Salts
on Selectivity
The importance of the
choice of salt for the mobile phase is frequently underestimated.
The nature of salt additives can have a critical effect on selectivity
(Figure 1). Here, a peptide with a phosphoserine
residue is far better retained than the corresponding peptide with
an aspartyl residue when a phosphonate salt is used but not when a
phosphate salt is used. As an alternative to solvents containing nonvolatile
salts, it has been proposed that ERLIC be performed with solvents
containing ammonium formate, weakly buffered in the range 2.0–2.2.[30] Those conditions separated phosphopeptides from
most unmodified peptides satisfactorily. The study did not consider
the behavior of unmodified peptides that contained numerous acidic
residues. Chien et al. subsequently noted[19] that such peptides were so abundant in the fractions of retained
peptides that they masked the phosphopeptides unless they were removed
from the fractions by IMAC enrichment. Analysis of the current set
of peptide standards with similar conditions demonstrates that the
complaint by Chien et al. was justified; peptides containing 3 or
4 Asp residues were poorly resolved from the standard with one phosphate
and peptides were retained in proportion to the number of acidic residues
(Figure 2a). When methylphosphonate salt is
used instead, then ionization of Asp residues is suppressed more effectively
and the standards with 3–4 Asp residues elute well before the
standard with 1 phosphate residue (Figure 2b).
Figure 1
Effect of salt on selectivity for phosphopeptides. The peptides
WAGGDASGK (red) and WAGG(pS)ASGK (blue) were separated using sodium
methylphosphonate (Na-MePO3) [top] or triethylammonium
phosphate (TEAP) [bottom] in the mobile phase. Column: PolySAX LP,
200 × 4.6 mm; 5 μm, 300 Å. Mobile phase: 20 mM of
the relevant salt, pH 6.0, containing 70% ACN. Flow rate: 1 mL/min.
Detection: 280 nm.
Figure 2
Use of different salts
for separation of tryptic peptides with
either Asp or pSer at the same sites. Peak identities were confirmed
by running the standards individually. Key to peptide standards: per
insert. Column: PolyWAX LP, 200 × 4.6 mm; 5 μm, 300 Å.
Flow rate: 1 mL/min. Detection: 280 nm. (A) ERLIC with ammonium formate:
Mobile Phase A: 20 mM ammonium formate, pH 2.2, with 70% ACN. Mobile
Phase B: 1 M ammonium formate, pH 2.2, with 10% ACN. Gradient schedule:
0–5′, 0% B; 5–35′, 0–100% B. (Note:
Standard 2P was run separately from the others under identical conditions).
(B) ERLIC with Na-MePO3: Mobile Phase A: 20 mM Na-MePO3, pH 2.0, with 70% ACN. Mobile Phase B: 300 mM TEAP, pH 2.0,
with 10% ACN. Gradient schedule: 0–5′, 0% B; 5–48′,
0–100% B.
Effect of salt on selectivity for phosphopeptides. The peptides
WAGGDASGK (red) and WAGG(pS)ASGK (blue) were separated using sodium
methylphosphonate (Na-MePO3) [top] or triethylammonium
phosphate (TEAP) [bottom] in the mobile phase. Column: PolySAX LP,
200 × 4.6 mm; 5 μm, 300 Å. Mobile phase: 20 mM of
the relevant salt, pH 6.0, containing 70% ACN. Flow rate: 1 mL/min.
Detection: 280 nm.Use of different salts
for separation of tryptic peptides with
either Asp or pSer at the same sites. Peak identities were confirmed
by running the standards individually. Key to peptide standards: per
insert. Column: PolyWAX LP, 200 × 4.6 mm; 5 μm, 300 Å.
Flow rate: 1 mL/min. Detection: 280 nm. (A) ERLIC with ammonium formate:
Mobile Phase A: 20 mM ammonium formate, pH 2.2, with 70% ACN. Mobile
Phase B: 1 M ammonium formate, pH 2.2, with 10% ACN. Gradient schedule:
0–5′, 0% B; 5–35′, 0–100% B. (Note:
Standard 2P was run separately from the others under identical conditions).
(B) ERLIC with Na-MePO3: Mobile Phase A: 20 mM Na-MePO3, pH 2.0, with 70% ACN. Mobile Phase B: 300 mM TEAP, pH 2.0,
with 10% ACN. Gradient schedule: 0–5′, 0% B; 5–48′,
0–100% B.We then compared the
retention of the same peptide standards under
conditions typical of AEX (Figure 3), employing
a gradient from ammonium acetate, pH 6, to 300 mM TEAP at pH 2 (both
with 10% ACN). Any increase in retention afforded by the double ionization
of phosphate groups is largely counteracted by the lack of retention
from hydrophilic interaction. Of greater concern is the potential
coelution with the singly and doubly phosphorylated peptides of the
peptide standards with two or more ordinary acidic residues, which
have full negative charge under these conditions. Retention times
of most of the peptides are greater with the PolySAX LP column (Figure 3b). This is as might be expected in view of the
greater charge density at pH 6 of a SAX material compared with a WAX
material. However, retention of the standards with 3 or 4 phosphate
groups or 4 Asp residues is as great or greater with the PolyWAX LP
column (Figure 3a). With such highly charged
analytes, the charge density of the stationary phase seems to be less
critical to retention.
Figure 3
High-pH AEX: Key to peptide standards, per Figure 2. Mobile Phase A: 20 mM ammonium acetate, pH 6.0,
with 10%
ACN. Mobile Phase B: 300 mM TEAP, pH 2.0, with 10% ACN. Gradient schedule:
As in Figure 2b. Flow rate: 1 mL/min. Detection:
280 nm. (A) Column: PolyWAX LP, 200 × 4.6 mm; 5 μm, 300
Å. (B) Column: PolySAX LP, 200 × 4.6 mm; 5 μm, 300
Å.
High-pH AEX: Key to peptide standards, per Figure 2. Mobile Phase A: 20 mM ammonium acetate, pH 6.0,
with 10%
ACN. Mobile Phase B: 300 mM TEAP, pH 2.0, with 10% ACN. Gradient schedule:
As in Figure 2b. Flow rate: 1 mL/min. Detection:
280 nm. (A) Column: PolyWAX LP, 200 × 4.6 mm; 5 μm, 300
Å. (B) Column: PolySAX LP, 200 × 4.6 mm; 5 μm, 300
Å.
Comparison of WAX vs SAX at Various pH Values
with Isocratic
Elution
Studies were performed using phosphate or phosphonate
salts, which buffer across most of the range of interest. The buffering
capacity is poor in some portions of the range. This seems less important
than the consistency in selectivity coming from use of the same salt.
The mobile phases contained either 10% ACN, for ordinary AEX operation,
or 70% ACN, where a significant degree of hydrophilic interaction
was superimposed upon the electrostatic effects. With 70% ACN the
mode is ERLIC at an operating pH of 3, where carboxyl groups are substantially
uncharged and electrostatic repulsion is significant. At higher pH
values the mode could be termed AEX-HILIC. The concentration of electrolyte
needed to form a reasonably complete double layer on the surface of
a charged stationary phase is about 20 mM in the overall mobile phase.[8,31] Accordingly, that concentration was used in this phase of the study.We then compared retention on WAX and SAX columns with a mobile
phase containing K-PO4 and 10% ACN (Figure 4A). With either column there is a modest increase in retention
of standard WAGGDASGK over the range pH 3–5 as its carboxyl
functional groups ionize. Retention of the phosphopeptides increases
more significantly between pH 5–7, the range of the phosphate
groups’ transition from one to two negative charges. The increase
is more significant with the SAX column. Thereafter retention remains
fairly constant with increasing pH values. The WAX column retains
its capacity at higher pH to a surprising degree, in view of the progressive
loss of charge density. We then performed separations on both columns
using 70% ACN for the mobile phase, using TEAP instead of K-PO4 out of concern for solubility (Figure 4B). An increase in retention similar to the previous experiment (Figure 4A) was noted over pH 3–5. Retention times
were appreciably longer than with 10% ACN. Presumably this is due
to the superimposed hydrophilic interaction. However, retention fell
off markedly on both columns above pH 5. Above pH 7 there was no significant
difference in retention between the phosphorylated peptides and their
unphosphorylated analogues.
Figure 4
Effect of pH on isocratic retention times. WAX
vs SAX: Columns
and flow rate: As in Figure 3. Mobile Phase
(isocratic): (A) 20 mM potassium phosphate, pH as noted, with 10%
ACN. (B) 20 mM TEAP, pH as noted, with 70% ACN. (C) 20 mM Na-MePO3, pH as noted, with 10% ACN. (D) 20 mM Na-MePO3, pH as noted,
with 70% ACN. Peptide standards: (1) WWGSGPSGSGGSGGGK (SAX, ⧫,
red; WAX, ⧫, blue); (2) WWGSGPSGSGG(pS)GGGK (SAX, ■,
red; WAX, ■, blue); (3) WAGGDASGK (SAX, ●, red; WAX,
●, blue); (4) WAGG(pS)ASGK (SAX, ▲, red; WAX,▲,
blue).
Effect of pH on isocratic retention times. WAX
vs SAX: Columns
and flow rate: As in Figure 3. Mobile Phase
(isocratic): (A) 20 mM potassium phosphate, pH as noted, with 10%
ACN. (B) 20 mM TEAP, pH as noted, with 70% ACN. (C) 20 mM Na-MePO3, pH as noted, with 10% ACN. (D) 20 mM Na-MePO3, pH as noted,
with 70% ACN. Peptide standards: (1) WWGSGPSGSGGSGGGK (SAX, ⧫,
red; WAX, ⧫, blue); (2) WWGSGPSGSGG(pS)GGGK (SAX, ■,
red; WAX, ■, blue); (3) WAGGDASGK (SAX, ●, red; WAX,
●, blue); (4) WAGG(pS)ASGK (SAX, ▲, red; WAX,▲,
blue).When the electrolyte was changed
to sodium methylphosphonate, with
either 10% or 70% ACN, tryptic phosphopeptides were much better retained
than tryptic unphosphorylated peptides, particularly over the pH range
6–7 for AEX (Figure 4C) and pH 5−6
for AEX-HILIC (Figure 4D). At a pH higher than
5, retention of phosphopeptides on the SAX column was nearly twice
as great as that on the WAX column. However, retention fell off above
pH 7 to about the same extent on both columns, as in Figure 4B. Retention of nonphosphorylated tryptic standard
peptides increased modestly with pH or remained about the same throughout
the range.Number and type of peptides identified from a HeLa cell lysate
via high-pH AEX. Column: PolySAX LP. Conditions: See Materials and Methods. See key for peptide categories.Number and type of peptides identified from
a HeLa cell lysate
via ERLIC. Column: (A) PolySAX LP; (B) PolyWAX LP. Conditions: See Materials and Methods. Key: See Figure 5.
Figure 5
Number and type of peptides identified from a HeLa cell lysate
via high-pH AEX. Column: PolySAX LP. Conditions: See Materials and Methods. See key for peptide categories.
From these results one
may draw the conclusions that, first, methylphosphonate
affords the best selectivity for phosphopeptides, at any pH. Second,
that at a pH higher than 5, retention of singly phosphorylated peptides
is greater on the SAX material than on the WAX material. However,
retention with WAX is still acceptable, and the selectivity between
phosphopeptides and acidic unmodified peptides seems to be at least
as good, if not better. Finally, depending on conditions, retention
of phosphopeptides reaches a maximum in the pH range 5–7 and
then declines on either material. Therefore, there is no benefit to
performing AEX of phosphopeptides at a pH higher than 7. Judging from
our data, a more appropriate pH is 6.
Analysis of a HeLa Cell
Lysate
To test our optimized
conditions on a biological sample, we chose tryptic peptides generated
from a HeLa cell lysate. The performance of the different ERLIC conditions
were again compared with AEX, this time by comparing the number and
nature of the peptides identified via two-dimensional LC-MS/MS. First,
a SAX column was eluted with conditions commonly used in the literature
for AEX of phosphopeptides. A gradient to 0.3 M phosphate was used
to ensure the elution of all phosphopeptides; however, this approach
failed to separate phosphopeptides well from acidic unmodified peptides
(Figure 5). The broad distribution of singly
phosphorylated peptides could reflect variations in their content
of Asp and Glu residues or the position of the phosphate group within
the peptide.[32] As expected from the results
described above, the selectivity improved when changing to the ERLIC
mode using the same column (Figure 6A) or a
WAX column (Figure 6B). As a result, ERLIC
identified significantly more phosphorylated peptides in the HeLa
digest (Figure 7A). While the AEX method identified
modestly more unmodified peptides, the two ERLIC runs each led to
the identification of 2.1 times more total phosphopeptides and, specifically,
5.4 times the number of multiply phosphorylated peptides using either
material (Figure 7B). The lower numbers of
phosphopeptides identified in the AEX mode can be explained by their
coelution with high numbers of unmodified peptides with 3 or more
acidic residues, which suppressed their identification in LC-MS. By
contrast, ERLIC effectively moved these unmodified peptides from the
phosphopeptide-containing part of the gradient to the early part of
the chromatogram. There was no serious difference in performance of
the WAX and SAX materials under ERLIC conditions (Figure 7B).
Figure 6
Number and type of peptides identified from
a HeLa cell lysate
via ERLIC. Column: (A) PolySAX LP; (B) PolyWAX LP. Conditions: See Materials and Methods. Key: See Figure 5.
Figure 7
(A) Unmodified and phosphorylated
peptides identified using SAX
and WAX with ERLIC or AEX. The numbers are summations of the numbers
in the various bars in Figures 5–7. (B) Phosphorylated peptides identified using SAX
and WAX with ERLIC or AEX. This is an expansion of the bars for phosphopeptides
in (A).
(A) Unmodified and phosphorylated
peptides identified using SAX
and WAX with ERLIC or AEX. The numbers are summations of the numbers
in the various bars in Figures 5–7. (B) Phosphorylated peptides identified using SAX
and WAX with ERLIC or AEX. This is an expansion of the bars for phosphopeptides
in (A).
Conclusions
ERLIC
is unequivocally superior to AEX for identification of tryptic
phosphopeptides from complex mixtures. While the SAX material has
greater retentivity than WAX material in the AEX mode at a pH higher
than 5, both materials have full charge density at the low pH used
for ERLIC. Their performance is then similar. Phosphopeptides are
less well-retained at such low pH conditions than under AEX conditions,
but are much better separated from acidic unmodified peptides. Consequently,
many more phosphopeptides are identified using ERLIC. The use of methylphosphonatesalts in the starting mobile phase affords superior selectivity for
phosphopeptides; however, an additional desalting step is then required.
That is no more troublesome than the extra affinity step that is needed,
when any other salt is used, to separate phosphopeptides from acidic
unmodified peptides. The subject of desalting ERLIC fractions has
been explored in detail by Loroch et al.[33,34] and Zarei et al.[35]To the best
of our knowledge, this is the first reported systematic
study of the retention of peptides in AEX as a function of pH. It
is not clear why retention decreases at pH values higher than 6 or
7, on the SAX as well as the WAX material. The effect is more pronounced
when a significant amount of hydrophilic interaction is present. Gilar
and Jaworski have calculated the retention coefficient of various
residues in peptides when eluted from Atlantis silica HILIC columns.[36] When electrostatic effects from charged amino
acids and surface silanols are discounted, retention due to most neutral
amino acids tends to increase from pH 3.0 to pH 4.5 and then decline
at pH 10, roughly consistent with the trends observed here. It is
possible that hydrophilic interaction decreases as the pH approaches
an extreme.
Authors: Tiannan Guo; Sze Sing Lee; Wai Har Ng; Yi Zhu; Chee Sian Gan; Jiang Zhu; Haixia Wang; Shiang Huang; Siu Kwan Sze; Oi Lian Kon Journal: Cell Mol Life Sci Date: 2010-10-16 Impact factor: 9.261
Authors: Marco L Hennrich; Vincent Groenewold; Geert J P L Kops; Albert J R Heck; Shabaz Mohammed Journal: Anal Chem Date: 2011-08-17 Impact factor: 6.986
Authors: Juan Antonio Vizcaíno; Richard G Côté; Attila Csordas; José A Dianes; Antonio Fabregat; Joseph M Foster; Johannes Griss; Emanuele Alpi; Melih Birim; Javier Contell; Gavin O'Kelly; Andreas Schoenegger; David Ovelleiro; Yasset Pérez-Riverol; Florian Reisinger; Daniel Ríos; Rui Wang; Henning Hermjakob Journal: Nucleic Acids Res Date: 2012-11-29 Impact factor: 16.971
Authors: Yusi Cui; Ka Yang; Dylan Nicholas Tabang; Junfeng Huang; Weiping Tang; Lingjun Li Journal: J Am Soc Mass Spectrom Date: 2019-07-08 Impact factor: 3.109
Authors: Bo Zhao; Mahalia A C Serrano; Meizhe Wang; Tianying Liu; Mallory R Gordon; S Thayumanavan; Richard W Vachet Journal: Analyst Date: 2018-03-12 Impact factor: 4.616